PlasmoDB 33 Released 30 June 2017

We are pleased to announce the release of PlasmoDB 33

PlasmoDB 32 Released 19 April 2017

We are pleased to announce the release of PlasmoDB 32

PlasmoDB 31 Released 8 March 2017

We are pleased to announce the release of PlasmoDB 31

EuPathDB is Hiring 21 February 2017

The Eukaryotic Pathogen Database resource (EuPathDB.org)

is a large, multi-institution project that develops scientific data-mining websites used by researchers worldwide to study selected microbial pathogens, including those responsible for malaria and enteric diseases.  At the request of the Bill & Melinda Gates Foundation, we are expanding this effort, with the goal of leveraging our extensive experience in the integration and analysis of pathogen genomics and functional datasets, so as to accommodate diverse clinical, epidemiological, socioeconomic, and geospatial information.  This new initiative focuses on the interplay between early childhood nutrition and the enteric infectious disease burden (cf. Mal-ED.fnih.org).

We anticipate hiring in the following areas:

Note that because EuPathDB staff work at several sites, hires could potentially be based at any of these institutions

Join our international team of 30+ software developers and biologists, combining the advantages of an academic environment with the rigor of developing a production system.  Make a difference to global public health!

PlasmoDB 30 Released 3 February 2017

We are pleased to announce the release of PlasmoDB 30

PlasmoDB 29 Released 13 October 2016

We are pleased to announce the release of PlasmoDB 29

PlasmoDB 28 Released 30 March 2016

We are pleased to announce the release of PlasmoDB 28

PlasmoDB 27 Released 19 February 2016

We are pleased to announce the release of PlasmoDB 27

PlasmoDB 26 Released 15 October 2015

We are pleased to announce the release of PlasmoDB 26

PlasmoDB 25 Released 23 July 2015

We are pleased to announce the release of PlasmoDB 25

PlasmoDB 24 Released 13 April 2015

Letter to the EuPathDB Community 19 February 2015

Dear colleagues -

We are writing to provide an update on the Eukaryotic Pathogen Genomics Resource (EuPathDB.org), which many hundreds of laboratories wrote to support in connection with our application for renewal as an NIH Bioinformatics Resource Center for Infectious Diseases.  We are pleased to report that the EuPathDB contract has now been renewed.

In addition to continuing to integrate the ever-increasing volume of Omic-scale datasets available for microbial eukaryotes, new functionalities anticipated over the coming months include:

• full integration of FungiDB into the EuPathDB family of databases
• reorganization of EuPathDB record pages, so as to improve navigability, better accommodate curated annotation (when available), represent alternative transcripts, summarize functional genomic results, etc
• better representation of experimental metadata, including phenotyping and clinical/field results
• enhanced functionality of the host response database (HostDB.org)
• improved handling of metabolic pathways, including incorporation of metabolomic datasets
• better support for orthology-based queries and cross-species inference
• implementation of workspaces enabling users to upload and analyze their own data (e.g. RNA-seq results)

The scope of this renewal extends beyond our previous mandate, which officially covered only biosecurity threats (Cryptosporidium, Entamoeba, Giardia, Toxoplasma, etc) and reemerging pathogens (e.g. Plasmodium).  This makes it easier for us to leverage EuPathDB infrastructure in support of the kinetoplastida, oomycetes, fungi, and other microbial eukaryotes, including both pathogenic and non-pathogenic species.

The scale of the EuPathDB award from NIH does not provide adequate funding for full support of the TriTrypDB or FungiDB projects (unfortunately) ... but the Wellcome Trust has agreed to consider an application covering these initiatives, augmenting our existing award for kinetoplastid resources.  We will be contacting users of these databases shortly for their support.

As always, we look forward to feedback from database users, via the 'Contact Us' link on all EuPathDB web sites, face-to-face discussions at major meetings, etc.

Brian P. Brunk -- EuPathDB Senior Project Manager
Christiane Hertz-Fowler -- Kinetoplastid Resources PI (on behalf of UK co-PIs)
Omar S. Harb -- EuPathDB Scientific Outreach Manager
Jessica C. Kissinger -- EuPathDB joint-PI
David S. Roos -- EuPathDB joint-PI, Kinetoplastid Resources co-PI, FungiDB co-PI
Jason E. Stajich -- FungiDB co-PI
Christian J. Stoeckert -- EuPathDB co-PI

PlasmoDB 13.0 Released 22 December 2010

The data set title below links to a full description and list of associated searches and GBrowse tracks.

Genomes:

Plasmodium coatneyi Hackeri - first release of this unannotated genome in PlasmoDB (AB Prasad Lab; Genbank version Jul 21, 2014)

Plasmodium reichenowi CDC - Newly-annotated. Strain name changed from Dennis to CDC (Otto et al.; GeneDB version Sept 3, 2014)

Proteomics:

Schizont Phosphoproteome (3D7)(2012)(Lasonder et al.) - Phosphoproteomic analysis of Plasmodium falciparum 3D7 schizont stage

RNA Sequencing:

Intraerythrocytic cycle transcriptome (3D7)(Hoeijmakers et al.) - RNA sequencing analysis of 8 time points during the P. falciparum 3D7 intraerythrocytic cycle. This dataset forms a pair with the previously integrated dataset "P. falciparum 3D7 MNase-Seq Nucleosome Occupancy (Barfai et al)", which was collected from the exact same batch of synchronized parasites.

Whole genome sequencing of isolates for SNP analysis:

Plasmodium vivax aligned genomic sequence reads - Hybrid Selection Project (Kidgell et al.) - Illumina whole genome sequencing of collections of clinical Plasmodium vivax samples (175 isolates) from diverse geographic regions represented by the NIAID-funded International Centers of Excellence for Malaria Research (ICEMRs), as well as non-ICEMR locations.

Plasmodium yoelii and Plasmodium falciparum aligned genomic sequence reads - 100 genomes project (Neafsey et al.)   -   Illumina whole genome shotgun sequencing of genomic DNA paired-end libraries of 55 P. falciparum isolates and P. yoelii 17X.

Plasmodium falciparum aligned genomic sequence reads - symptomatic malaria isolates (Plowe et el.) - Whole genome sequencing of isolates collected from symptomatic malaria patients.

    Improvements and updates:

BLAST was updated to the latest NCBI version 2.2.30.

GBrowse performance is improved following EuPathDB infrastructure changes.

PlasmoDB 12.0 Released 10 September 2014

• P. falciparum phosphoproteomic data: Data was generated from tightly synchronized ring, trophozoites, and schizonts (Pease et al.). View experimental details and links to searches in the dataset section. 

• P. falciparum Polysomal and steady-state asexual stage transcriptomes:  Analysis of the levels of steady-state mRNA and polysome-associated mRNA at the ring, trophozoite, and schizont stages of the intra-erythrocytic cycle of P. falciparum 3D7 using Illumina sequencing (Bunnik et al.). View experimental details and links to searches in the dataset section. 

• P. berghei transcript expression: Illumina-based sequencing of RNA from five different stages of P. berghei ANKA development (4h Ring, 16h Trophozoite, 22h Schizont, Gametocytes, 24h Ookinete) (Hoeijmakers et al. unpublished). View experimental details and links to searches in the dataset section.

PlasmoDB 11.1 Released 6 May 2014

• ChIP-seq data from a EuPathDB-funded project: Genomic position of nucleosome binding in P. falciparum 3D7 was assayed over the intraerythrocytic cycle using ChIP-seq.  This data is represented as coverage plots in the genome browser.  View experimental details in the dataset section. 

• P. falciparum quantitative proteomic data: Data was generated from tightly synchronized ring, trophozoites, and schizonts (Pease et al.). View experimental details and links to searches in the dataset section. 
  

PlasmoDB 11.0 Released 30 January 2014

• Serum antibody levels determined by protein microarray (Crompton et al.).  For full attribution and available searches please see the dataset details.  This data can be found under a new search category called "Host Response" that has been added to PlasmoDB under the heading "Identify genes By" on the home page.  The search against this dataset offers versatile sample grouping based on metadata (ie. age, sex, disease state, etc...) and returns genes whose protein products were the target of antibodies found in the serum of malaria patients.

• The genome sequence and annotation of Plasmodium yoelii yoelii 17X (a non-lethal 17X clone).  Additional information about all genomes may be viewed in the dataset section of PlasmoDB.  Note that this genome was graciously provided by GeneDB pre-publication.  Please consult with the Principal Investigator before undertaking large scale analyses of the annotation or underlying sequence.  This genome sequence and annotation will replace the previous 17XNL sequence and annotation as the reference 17X genome. The genome sequence and annotation of the previous 17XNL has been temporarily removed but access is still available through the previous version of PlasmoDB. 

• EuPathDB is pleased to announce the release of a beta version of HostDB - a resource dedicated to integrating functional host response data.  The beta release includes the human and mouse genomes and two datasets (RNA-Seq and quantitative proteomics) examining the host response to Toxoplasma infection.  We look forward to expanding this database in data content and functionality.  We encourage you to explore HostDB and provide us with your feedback. 

EuPathDB Annual Workshop 14 January 2014

We are pleased to announce the 9th annual EuPathDB workshop to be held in Athens, Georgia, USA from June 15 to Wednesday, June 18, 2014.  

Please note that the workshop expenses, in addition to room and board costs are covered by EuPathDB (see cost and fees section below). 

Come learn how to effectively use EuPathDB resources and mine available data to help guide your research.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

The workshop will cover all of our component databases (EuPathDB, AmoebaDB, CryptoDB, GiardiaDB, MicrosporidiaDB, PlasmoDB, PiroplasmaDB, ToxoDB, TrichDB, TriTrypDB and OrthoMCL), and will run from 6:00PM (18:00) on Sunday, June 15 to 5:00PM (17:00) on Wednesday, June 18, 2014.

The application deadline is February 28, 2014 and the course is limited to 30 participants.

Who should apply:  This workshop is intended to be a 3 day thorough and intensive introduction to database resources that are part of the EuPathDB.org Bioinformatics Resource Center (EuPathDB, AmoebaDB, CryptoDB, GiardiaDB, MicrosporidiaDB, PlasmoDB, PiroplasmaDB, ToxoDB, TrichDB, TriTrypDB and OrthoMCL). The ideal candidate would have a need to become an expert user of one or more of these database resources and presumably has a bioinformatics research problem that they might work on as part of their training while attending the course. Preference will be given to applicants that are in a position to benefit most from intensive training and that are in a position to return to their home institution and transfer their newly acquired knowledge to others. Evaluation of the applications will focus heavily on your responses to the questions asked on the application page and on letters of recommendation.
     
Costs and Fees: The course is free. Housing (double occupancy), all training materials and lunches are covered. Attendees are expected to provide their own transportation to the course and pay for a few of their meals. Letters of acceptance will be mailed early to facilitate the solicitation of outside travel funds.

Hotel room charges for a shared room will be paid by EuPathDB for the nights of June 15 through June 18. Attendees who would like to have a private room will need to pay the difference of $47 per night plus tax.   

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

If you have any questions or concerns please email help@eupathdb.org

   

 

PlasmoDB 10.0 Released 25 September 2013

• The following genomes have been updated.  Additional information about all genomes may be viewed in the Dataset section of PlasmoDB.  Note that many of these genomes have been graciously provided prepublication to the scientific community - please consult with the Principal Investigator before undertaking large scale analyses of the annotation or underlying sequence:

• Plasmodium berghei ANKA (GeneDB version 03-01-2013)
• Plasmodium chabaudi chabaudi (GeneDB version 03-01-2013)
• Plasmodium cynomolgi B (GenBank version 09-19-2012)
• Plasmodium falciparum 3D7 (GeneDB version 03-01-2013)
• Plasmodium falciparum IT (GeneDB version 03-01-2013)
• Plasmodium knowlesi H (GeneDB version 03-01-2013)
• Plasmodium vivax SAL1 (GeneDB version 05-01-2013)
• Plasmodium yoelii yoeliiYM (GeneDB version 03-01-2013)

• P. yoelii salivary gland RNA sequence data from wild type and Puf2 knockout P. yoelii 17XNL parasites (Lindner et al.). 

• Genes may be identified based on their fold change difference between wild-type and knockout parasites or based on their percentile expression in each sample using the RNA Seq Evidence search page in PlasmoDB. 

• Graphical representation of this data is available in the expression section of gene pages.  

• Data from this experiment is available as coverage plots in the genome browser and evidence of intron spanning reads is indicated in the "Splice Site Junctions" track.  In this example a genome browser region shows differential expression of a gene and evidence of an alternative gene model that differs from the official annotation.

• Total and putative surface proteomes of P. falciparum N54 and P. yoelii 17XNL Salivary gland sporozoites (Lindner et al.).  Peptides from P. falciparum N54  samples were mapped to the P. falciparum 3D7genome and peptides from P. yoelii 17XNL were mapped both to the 17XNL and P. berghei genomes. 

• Genes with mapped peptides may be identified using the Mass Spec evidence search page in PlasmoDB.  

• Peptide evidence is also displayed in the protein section of gene pages and in the genome browser by turning on the track - "Plasmodium MS/MS Peptides Salivary gland sporozoite total and surface proteomes (Lindner and Swearingen et al.)".

GBrowse tracks remain open between sessions:

• EuPathDB now stores GBrowse track configurations between sessions for registered users who log into any EuPathDB site. The EuPathDB login is now integrated with the GBrowse login so that your previous session's GBrowse tracks are displayed each time you return to a EuPathDB site.

New streamlined look for choosing expression data sets (microarray, RNA-Seq):

• A new interactive table for choosing expression data sets lists datasets, searches for each dataset and the organism that the data is aligned to. Use the table's filter function to limit the data set list based on author name, parasite life stages, etc. Click on an icon under "Choose a search" to collapse the table and display the data set's search page with its parameter list below the collapsed table.

On-page help for expression search pages:

• Search parameters appear on the left and are arranged in a sentence that helps you choose parameter values.

• A help graphic and text appear on the right. To help you interpret your parameters choices, the graphic changes to reflect your parameter settings.

Improved Strategy Panel for viewing and editing steps:

• The graphic interface of the strategy panel has been updated.  View the results of a strategy step by clicking anywhere inside the box representing that step. To edit the parameter values for that step, click on the EDIT icon that appears in the corner of each strategy step box when hovering over the strategy panel.

PlasmoDB 9.3 Released 10 March 2013

We are pleased to announce the release of PlasmoDB 9.3

New data in this release:

• Transcriptional variation across subclonal strains derived from P. falciparum strains 3D7, 7G8, D10 and HB3 (Rovira-Graells et al.).  This data may be used to search for genes based on fold change, percentile expression and copy number variation (available in the microarray query section under the heading "Transcriptional variation of P. falciparum strains").  In addition, expression graphs are available on individual gene pages in the transcript expression section under the heading "Transcriptional Variation of P. fal parasite lines".  Note that graphs representing lineage-specific expression over the intraerythrocytic life cycle may be displayed by selecting the appropriate check box to the right of the graphs.

• High throughput sequencing (HTS) of 65 clinical isolates from Gambia (Amambua-Ngwa et al.).  This data may be used to identify single nucleotide polymorphisms (SNPs) between the sequenced isolates:

• SNPs between all or a subset of strains from this study can be defined based on a comparison with each other or with strains from other studies.  This search strategy defines all SNPs present in strains from this study. 

• Genes may defined based on their relation to the above defined SNPs using the genomic colocation query, for example:
  • Gene that contain any of the SNPs
  • Genes that are located downstream of a SNP (in this example 200 nucleotides downstream)
  
  

• View and download SNP records generated from pairwise comparisons of isolate sequences.

• Search for genes based on the characteristics of SNPs contained within the gene. This dataset can be queried by clicking on "HTS SNP Characteristics".

• Search for individual SNP records based on criteria such as SNP ID, strain, genomic location, etc.

• View sequencing read pileups, reads aligned to the P. falciparum 3D7 genome, and read density plots in GBrowse using the options under the Select Tracks heading: HTS SNPs, pfal3D7_Conway_HTS_SNP.

• View SNP information for individual genes on record pages. 

• View individual HTS SNPs aligned to the genome with the GBrowse track: HTS SNPs by coding potential.

• Metabolite data generated from P. falciparum parasites and infected and uninfected red blood cells.  Experimental details are available in the data set section of PlasmoDB.  This data was generated as part of the EuPathDB-funded driving biological project and made available pre-publication (Llinas, Baska and Lewis).  Data from this experiment may be searched based on metabolite levels and viewed graphically on compound pages.

• Two new data types with searches have been added in this release: compounds and metabolic pathways.  This beta-release of Compound and Metabolic Pathways data sets incorporates KEGG pathways and a subset of PubChem records. Future releases will include compounds for additional metabolites and small molecules, and pathways from other sources such as MPMP, MetaCyc, etc. Please explore the site and contact us with your feedback.

• Metabolic Pathways may be searched based on pathway Name/ID, genes, or compounds.

• Compounds may be searched based on compound ID, text (synonym, InChI, etc.), enzymes, metabolic pathway, molecular formula, molecular weight or metabolite levels.

New Functionality:

PCR Primer Design tool added to GBrowse.

Design PCR primers to any region of the genome using this interactive, graphic interface. To reach this tool, open the PlasmoDB Genome Browser at your genomic region of interest, choose "Design PCR primers" from the dropdown menu and click "GO".  To design primers, focus on a PCR product size range by highlighting the area on the scale, then enter your preferred PCR parameters in the text boxes and click Design Primers.

EuPathDB Annual Workshop 20 January 2013

We are pleased to announce the 8th annual EuPathDB workshop to be held in Athens, Georgia, USA from June 2-5, 2013.

Please note that the workshop expenses, in addition to room and board costs are covered by EuPathDB (see cost and fees section below).

Come learn how to effectively use EuPathDB resources and mine available data to help guide your research.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

The workshop will cover all of our component databases (EuPathDB, AmoebaDB, CryptoDB, GiardiaDB, MicrosporidiaDB, PlasmoDB, PiroplasmaDB, ToxoDB, TrichDB, TriTrypDB and OrthoMCL), and will run from 6:00PM (18:00) on Sunday, June 2 to 5:00PM (17:00) on Wednesday, June 5, 2013.

The application deadline is February 18, 2013 and the course is limited to 30 participants.

Who should apply: This workshop is intended to be a 3 day thorough and intensive introduction to database resources that are part of the EuPathDB.org Bioinformatics Resource Center (EuPathDB, AmoebaDB, CryptoDB, GiardiaDB, MicrosporidiaDB, PlasmoDB, PiroplasmaDB, ToxoDB, TrichDB, TriTrypDB and OrthoMCL). The ideal candidate would have a need to become an expert user of one or more of these database resources and presumably has a bioinformatics research problem that they might work on as part of their training while attending the course. Preference will be given to applicants that are in a position to benefit most from intensive training and that are in a position to return to their home institution and transfer their newly acquired knowledge to others. Evaluation of the applications will focus heavily on your responses to the questions asked on the application page and on letters of recommendation.

Costs and Fees: The course is free. Housing, all training materials and most meals are covered. Attendees are expected to provide their own transportation to the course and pay for a few of their meals. No travel funds are available. Letters of acceptance will be mailed early to facilitate the solicitation of outside travel funds. Hotel room charges will be paid by EuPathDB from June 2 through 11:00am June 6 (Note: course ends at 5PM on June 5). Participants traveling from abroad may be able to arrive a day early or stay a day late as needed to accommodate travel arrangements.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

If you have any questions or concerns please email help@eupathdb.org

DEVELOPMENT OF A MOLECULAR BARCODE FOR PLASMODIUM VIVAX 2 November 2012

The Harvard School of Public Health and Broad Institute including Professors Sarah Volkman, Manoj Duraisingh, Daniel Hartl, Daniel Neafsey, Pardis Sabeti, and Dyann Wirth with funding support from the Bill and Melinda Gates Foundation (BMGF) are in the process of developing a molecular barcode tool for Plasmodium vivax with the collaboration of the malaria community. We invite members of this community who are interested in either collaboration or potential application of this tool to participate in this endeavor.

Additional information is available in this downloadable document.

PlasmoDB 9.1 Released 31 August 2012

• P. falciparum schizont phosphoproteomic data (Solyakov et al.).  This data can be searched by choosing "Schizont Phospho-proteomic analysis (Solyakov et al.)" in the P. falciparum section of the Mass spec. evidence search page. Peptides from this dataset are displayed on gene pages in the Protein section and in the Genome Browser by turning on the data track: Pf. Mass Spec - Schizont Pohspho-proteomic analysis (Solyakov et al.).       
  

PlasmoDB 9.0 Released 23 May 2012

• The following genomes and annotation have been updated from GeneDB:

• P. falciparum 3D7 (February 2012 GeneDB version) Note: The new P. falciparum gene IDs have been fully integrated in this release.  Old gene IDs are still displayed on gene pages and searches can still be performed with old gene IDs.
• P. falciparum IT (February 2012 GeneDB version)
• P. berghei  ANKA (March 2012 GeneDB version)
  
• P. chabaudi AS (March 2011 GeneDB version) Note: A newer version of this genome and annotation will be included in the next release of PlasmoDB.

• Strand-specific, amplification-free transcriptome sequence (FRT-Seq) from P. falciparum 3D7 parasites (Pooled red blood cell stage).  This data was graciously provided prepublication by the Berriman and Newbold labs and may be visualized as a track in the genome browser.  Here is an example genome browser view of chromosome 6 with the "Pf RNA-Seq - Sanger FRT (log2) [Newbold / Berriman labs]" turned on.  Note that histogram colors correspond to transcript direction (blue = forward strand, red = reverse strand).

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   Genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

PlasmoDB 8.2 Released 11 January 2012

• P. vivax Schizont stage proteome from human blood samples (Roobsoong et. al.).  This data can be searched by choosing "Schizont stage proteome from human blood sample (Roobsoong et al.)" in the P. vivax section of the Mass Spec. Evidence search page. In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  This search strategy identifies all P. vivax genes with mass spec evidence from this study.

• P. falciparum nuclear and cytosolic fractions from rings, trophozoites, and schizonts graciously provided prepublication by Till Voss and colleagues.  This data can be searched by choosing "P. falciparum cytoplasmic and nuclear fractions from rings, trophozoites and schizonts (3D7) (Oehring and Woodcroft et al. - unpublished)" in the P. falciparum section of the Mass spec. evidence search page. In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  This search strategy identifies all P. falciparum genes with mass spec evidence from this study. 

• P. falciparum blood stage phosphoproteome (Treeck & Sanders et. al.).  This data can be searched by choosing "Blood stage phosphoproteome and total proteome (3D7) (Treeck & Sanders et al.)" in the P. falciparum section of the Mass spec. evidence search page. In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  This search strategy identifies all P. falciparum genes with phospho mass spec evidence from this study.

• P. falciparum ChIP-sequence data from the histone variant H2Bv (three time points) and  CenH3 (schizonts) represented as coverage plots in the genome browser.  This data was graciously provided prepublication by the Stunnenberg group.

• Genome-wide expression level polymorphisms (ELPs) from a genetic cross between phenotypically distinct parasite clones of P. falciparum (HB3 and Dd2) (Gonzales et. al.). This data may be searched and visualized in many ways:

• Genes may be identified based on their association to genomic segments, expression profile similarity or similarity of genetic association.  These searches are based on the microarray expression profiles generated in each of the progeny and can be accessed in the microarray search page under the heading "eQTL studies on Hb3 X Dd2 progeny (Ferdig)". 

• Genomic segments can be identified based on their association to genes.  This search is available by clicking on "P.f. eQTL HB3-Dd2 cross (segments by association to genes)" under the heading "Genomic Segments" in the "Identify other data types" section of the PlasmoDB home page.
  

• Regions/spans that are associated by eQTL are displayed in a table on gene pages (example gene page). The table "Regions/Spans associated by eQTL experiment on HB3 x DD2 progeny" includes a column for haplotype blocks associated the gene, the coordinates of the haplotype block, LOD scores, and links to searches for genes contained within the region or associated with the region.

• Both microsatellites and haplotype blocks are available as tracks in the genome browser. 
  

• Improved linking to the Rodent Malaria Genetically Modified (RMgm) parasites database.  A dedicated "Phenotype" table is now available on gene pages with information about the genetic modification and linkouts to PubMed and the RMgm database.  As an example, you can scroll down and expand the table under the heading "Phenotype" on the  gene page for a putative P. berghei guanylyl cyclase.
  

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   Genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

• New Gene IDs -- Please read the news item from GeneDB regarding assignment of new P. falciparum gene IDs. We will be updating to these new IDs in the next release. Rest assured that both PlasmoDB and GeneDB will proper mapping of old IDs to the new ones (in other words, you will always be able to search with the old or new IDs). Currently in PlasmoDB we are displaying the new Gene ID next to the old one at the top of gene pages (old ID/new ID).     

Version 1 of P. yoelii yoelii YM is now available on GeneDB! 4 January 2012

Verson 2 of P. falciparum IT is now available on GeneDB! 17 November 2011

A new sequence version of P. falciparum 3D7 is now available on GeneDB! 24 September 2011

PlasmoDB 8.0 Released 21 July 2011

• Sequence and annotation of the P. falciparum IT strain produced by the Parasite Genomics Group at the Wellcome Trust Sanger Institute with funding from the EVIMalaR Consortium (a European Commission Funded Network of Excellence).  While this data has been graciously provided prepublication to the community its usage for large scale genomic analysis is bound by a data usage policy.

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   A full description of new pathways is available here and genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

• You can now view intron/exon boundaries based on available RNA sequence data.  boundary determination was performed using the RNA-Seq Unified Mapper (RUM). To view intron/exon boundary calls, turn on the "RNA-seq alignments RUM Intron" track in the genome browser.  Here is a link to a gene that is predicted to have multiple splice variants based on the annotation provided by GeneDB with the RUM intron tracks turned on.  To get additional information mouse over the tracks and/or the track names.

PlasmoDB 7.2 Released 3 May 2011

• P. falciparum mRNA half-life data intraerythrocytic developmental cycle (Shock et. al.) is now available as mRNA expression and half-life graphs on gene pages.  To view this data visit any gene page and scroll down to the section called "mRNA half-lives during intraerythrocytic development - 3D7 post treatment with actD" in the Expression section of any gene page.

• P. falciparum genetic diversity estimate graph is provided in the genome browser based on Nygaard et. al.

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   A full description of new pathways is available here and genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with an AP-2 like motif within 1000 bp of their 5' end.

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account
  
• How to run a text search
• How to use Favorites
• How to find a DNA motif
• How to use genomic co-location

Plasmodium genome sequencing project update 25 March 2011

PlasmoDB 7.1 Released 18 November 2010

• P. falciparum blood stage proteomics data (trophozoites and early and mature gametocytes) from Silvestrini et. al.  This data can be searched from the Mass spec. evidence search page under the heading "Protein Expression" -- listed under Plasmodium falciparum and selecting "Blood Stage Proteome - Trophozoites, Early Gametocytes (gct I/II) and/or Mature Gametocytes (gct V)".  In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  An example search strategy that identifies genes that have mass spec evidence in the early gametocytes but not in trophozoites or mature gametocytes can be accessed and modified here.
  

• You can now add publications to your user comments using their Digital Object Identifier (DOI) numbers.  To view a list of all genes that have a user comment in PlasmoDB, click here.

• You can view microarray oligo mapping for all arrays with data in PlasmoDB.  Oligo mapping can be viewed in the Genome Browser by turning on tracks under the heading "Expression Microarray Probes".
  

Driving Biological Projects awarded 20 October 2010

• The Toxoplasma oocyst transcriptome and proteome
  John Boothroyd, Matt Bogyo (Stanford) & Pat Conrad (UC Davis)
  This project is expected to yield expression data from an important, but inaccessible, life cycle stage (1 yr).
  
  
• A comprehensive catalog of the T. gondii & N. caninum parasite & infected host cell transcriptome & proteome
  Brian Gregory (Univ. Pennsylvania) & Jonathan Wastling (Univ. Liverpool)
  This project will produce an immense volume of sequence data, driving database improvements for handling 'next-gen' sequencing, non-coding RNAs, and interrogating host & pathogen datasets in parallel (2 yr).
  
  
• Dissection of Plasmodium falciparum genetic crosses by mass spectrometry-based metabolite QTL
  Manuel Llinás (Princeton) & Michael Ferdig (Notre Dame)
  This project is expected to improve handling of genetic mapping data, incorporation of metabolomics results (integrated with pathway maps), and linking of specific genetic loci with metabolite abundance (2 yr).
  
  

PlasmoDB 7.0 Released 21 September 2010

• Updated sequence and annotation for Plasmodium falciparum, P. chabaudi, P. knowlesi and P. berghei was obtained from the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute.  Additional details may be viewed here.

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   A full description of new pathways is available here and genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.
  

• Plasmodium falciparum, P. vivax, P. yoelii, P. berghei and P. chabaudi predicted ApiAP2 transcription-factor (TF) binding site data.  This data was graciously provided prepublication by Dr. Manuel Llinas.  Gene with predicted binding sites to each ApiAP2 TF may be identified using the TF binding site search available via the Transcript Expression section of PlasmoDB.  Search parameter such as distance from the 5' end, number of TF binding sites and probability score can be adjusted as needed.  In addition, TF binding sites can be viewed in the genome browser with additional information available when mousing over TF binding site graphics.  An example genome browser page may be viewed here.

• P. falciparum RNA-sequence data from the intraerythrocytic life cycle.  This data was graciously provided prepublication to the community via PlasmoDB by Dr. Richárd Bártfai, Wieteke A.M. Hoeijmakers and Dr. Hendrik G. Stunnenberg.  Searches against this data may be accessed from the RNA-seq evidence section in the Transcript Expression section of PlasmoDB.  RNA-seq data may also be viewed on individual gene pages where a graphical representation of the gene's expression profile throughout the time points of this study is presented.   In addition,  RNA-seq coverage graphs can be viewed through the PlasmoDB genome browser.
  

• P. falciparum ChIP-sequence data from the intraerythrocytic life cycle.  ChIP was performed using antibodies to H2A.Z, H3K9ac & H3K4me3. This data was graciously provided prepublication to the community via PlasmoDB by Dr. Richárd Bártfai, Wieteke A.M. Hoeijmakers and Dr. Hendrik G. Stunnenberg.  This data can be viewed through the PlasmoDB genome browser.

• P. falciparum RNA-sequence data of lab-adapted field parasites from malaria-infected pregnant women and children.  This data was graciously provided prepublication to the community via PlasmoDB by Drs. Marissa Vignali and Patrick E. Duffy.  Searches against this data may be accessed from the RNA-seq evidence section in the Transcript Expression section of PlasmoDB.  RNA-seq data may also be viewed on individual gene pages where a graphical representation of the gene's expression profile throughout the time points of this study is presented.   In addition,  RNA-seq coverage graphs can be viewed through the PlasmoDB genome browser.

• Improved organization of the microarray search page.
• The search strategy window is now resizable.

PlasmoDB 6.5 released 15 July 2010

• A proteomics dataset for P. falciparum from 42 and 48 hrs post infection kindly provided prepublication by Paul Bowyer and Matthew Bogyo, Stanford University School of Medicine.
• P. falciparum SNP calls for 186 culture adapted strains provided by Jianbing Mu and Xinzhuan Su, NIH.
  Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nat. Genet. 2010 Mar;42(3):268-71 Mu et al.

PlasmoDB 6.4 released 13 May 2010

• PiggyBac insertion sites in P. falciparum (NF54) from Balu et. al. are available via the genome browser.  To view insertion sites turn on the track called "P. falciparum piggyBac Transposable Elements" under the heading "Insertions".  Here is a quick link to the genome browser with a region with insertions: piggyBac insertions in chromosome 11. 


• ChIP-chip data using histone H4 antibodies from Westenberger et. al. are available via the genome browser under the ChIP on chip heading. You may view tracks for different RBC life stages as in this example.


• Nucleosome positioning data from Ponts et. al.  are available via the genome browser under the ChIP-seq heading.  You may view tracks for different time points during the RBC life cycle as in this example.

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative vaccine candidates.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative vaccine candidates (unweighted)

Putative vaccine candidates (Weighted)


3. "My Favorites" (new in this release) allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 


4. We now provide prominent linkouts to GeneDB from PlasmoDB gene pages when there is an update in GeneDB not yet available in PlasmoDB.  This feature enables PlasmoDB users to have easy access to the most up-to-date information.  It is important to highlight that your comments on gene pages in PlasmoDB constitute one of the tools made available to the annotators at GeneDB to improve and enhance the genome annotation.

EuPathDB Scientific Working Group 31 March 2010

PlasmoDB new features 15 March 2010

• The gray tool bar at the top of all PlasmoDB web pages has been enhanced to include a link to the "My Basket" feature including an indication of how may items are in the basket.
• The genome browser has been updated to version 1.7, which offers enhanced features and stability. 
• Weighted searches are now available.  This feature allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results. 

PlasmoDB 4.4 is no longer available 15 February 2010

EuPathDB Driving Biological Projects 4 February 2010

PlasmoDB 6.3 released 22 December 2009

• P. falciparum transcriptome sequencing (RNA-seq) profiles.  This data was graciously provided to PlasmoDB prepublication and will soon appear in press: New insights into the blood stage transcriptome of Plasmodium falciparum using RNA-Seq.  Thomas D. Otto, Daniel Wilinski, Sammy Assefa, Thomas M. Keane, Louis R. Sarry, Ulrike Bohme, Jacob Lemieux, Bart Barrell, Arnab Pain, Matthew Berriman, Chris Newbold, Manuel Llinas.  Molecular Microbiology (in press).  You can search for genes based on this data by going to the "P. falciparum transcriptome sequencing (RNA-seq) profiles" search under "Transcript Expression" in PlasmoDB.

• P. falciparum transcription profile of wild-type and Sir2a and Sir2b knock-out parasites.  Using this search you can find genes that are differentially expressed between wild-type and knock-out parasites during the intraerythrocytic life-cycle.  You can search for genes based on this data by going to the "Microarray Evidence" search under "Transcript Expression" in PlasmoDB.   Details of this study can be found here:  Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duffy MF, Silva LM, Scherf A, Ivens A, Speed TP, Beeson JG, Cowman AF. Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol. 2009 Apr 14;7(4):e84.

• Transcription profiling of Plasmodium falciparum after exposing drug-selected mutants to short term CQ treatment.  Identify genes differentially expressed during chloroquine treatment.  You can search for genes based on this data by going to the "Microarray Evidence" search under "Transcript Expression" in PlasmoDB. Details of this study can be found here: Jiang H, Patel JJ, Yi M, Mu J, Ding J, Stephens R, Cooper RA, Ferdig MT, Su XZ. Genome-wide compensatory changes accompany drug- selected mutations in the Plasmodium falciparum crt gene. PLoS One 2008 Jun 25;3(6):e2484.

• P. falciparum HP1 chromatin immunoprecipitation data.  You can search for genes based on this data by going to the "P.f ChIP on chip evidence" search under "Transcript Expression" in PlasmoDB. Details of this study can be found here: Flueck C, Bartfai R, Volz J, Niederwieser I, Salcedo-Amaya AM, Alako BT, Ehlgen F, Ralph SA, Cowman AF, Bozdech Z, Stunnenberg HG, Voss TS.  Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS Pathog. 2009 Sep;5(9):e1000569. Epub 2009 Sep 4.

• Chromatin immunoprecipitation to identify histone modifications (H3K9me3, H3K9Ac, H3K4me3, H4K20me3) in P. falciparum wild type and Sir2 knock-outs. You can search for genes based on this data by going to the "P.f ChIP on chip evidence" search under "Transcript Expression" in PlasmoDB. Details of this study can be found here:  Lopez-Rubio JJ, Mancio-Silva L, Scherf A. Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites. Cell Host Microbe. 2009 Feb 19;5(2):179-90.

Working with Parasite Database Resources Workshop (April 17-21, 2010) 20 November 2009

PlasmoDB 6.2 released 13 November 2009

• P.  falciparum and P. vivax proteomics from clinical samples graciously provided prior to publication by Dr. Utpal Tatu (Department of Biochemistry, Indian Institute of Science, Bangalore, India). This data may be accessed using the "Identify Genes based on Mass Spec. Evidence" query and combined with other searches in PlasmoDB.

Important announcement regarding microarray data in PlasmoDB 26 October 2009

PlasmoDB 6.1 released 25 September 2009

• P.  falciparum intraerythrocytic expression profiles from infected patients (Lemieux et. al.) -- data available on gene pages, for example, click here and scroll down to the expression section.

• Now after you perform a BlastN against genomic sequence you can link from the blast output to the correct coordinates in the genome browser.  This allows you to explore annotation and other functional data in relation to your BLAST hits.
• Linkouts to Gene Ontology annotation predictions at Plasmodraft have been updated. (Bréhélin et. al.).
• Linkouts to the Malaria Parasite Metabolic Pathways resource (Hagai Ginsburg).
• The type ahead feature has been implemented for GO term, EC number and Interpro domain searches.
• You can now edit or delete your user comments.
• You can now modify your user profile, change your password or your email address.

PlasmoDB 6.0 released 14 July 2009

The EuPathDB team is happy to announce the release of PlasmoDB 6.0.

This release includes several new and updated data sets (many prepublication), a new user interface with added functionality and a graphical strategy system for building complex searches.

The new user interface contains many new features including:

• A new search strategy interface that enables users to more easily construct complex searches.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation.
• Files can now be uploaded and provided to the community via the file repository section.

New and updated Data:

• P. falciparum reannotation integrated as the official annotation in PlasmoDB (See news item dated 1 February 2008 for details on the reannotation effort).
• P. falciparum High density genotyping array (HD Array) from the Broad Institute (Unpublished).
• P. vivax intraerythrocytic microarray life-cycle (Bozdech et. al.).
• P. vivax microarray from patient samples (Westenberger and Winzeler, unpublished).
• P. chabaudi new 8X assembly and reannotation (Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute, unpublished).
• P. yoelii published gene calls appear as provisional genes in the genome browser (Vaughan et. al.).
• P. yoelii oocyst and salivary gland microarray data (Zhou et. al.).
• Isolate data from GenBank is now integrated and searchable.

Additional features:

• Linkouts are now provided from genes with mutant information in the Genetically Modified Rodent Malaria Parasites database.
• Linkouts are provided to Gene Ontology annotation predictions at Plasmodraft. (Bréhélin et. al.).

  The previous version of PlasmoDB may still be accessed here.

EuPathDB to take on the kinetoplastida 1 December 2008

Fifth updated snapshot of the reannotation of the P. falciparum 3D7 genome 18 November 2008

The effort to systematically update the annotation for P. falciparum 3D7 genome started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Institute (WTSI) and the EuPathDB team. The Wellcome Trust and Burroughs Wellcome Fund-sponsored workshop was held in Hinxton, UK and was attended by nearly 30 Plasmodium researchers contributing expertise in various aspects of Plasmodium biology, plus more than 10 bioinformatics support staff from the Artemis, GeneDB and EuPathDB teams. Ongoing annotation and error checking is being carried out by the GeneDB group from WTSI.

For further information please refer to the February 1st, 2008 news item (below).

PlasmoDB publication in Nucleic Acid Research 4 November 2008

PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2008 Oct 31. Aurrecoechea C, et al.

PlasmoDB 5.5 released 16 September 2008

The EuPathDB team is happy to announce the release of PlasmoDB 5.5.

New Data:

• Proteomics:
• P. falciparum purified merozoite proteomics data provided prepublication by the Leiden Malaria Group.
• P. yoelii liver stage proteomics (Tarun et al. Proc. Natl. Acad. Sci. U.S.A. (2008) vol. 105 (1) pp. 305-10).

• Microarray:
• P. yoelii liver, mosquito, and red cell stage expression data (Tarun et al. Proc. Natl. Acad. Sci. U.S.A. (2008) vol. 105 (1) pp. 305-10).
• P. falciparum expression data from infected patients (Daily et al. Nature 2007 Dec 13;450 (7172):1091-5).

• Population Biology:
• Isolate data from P. falciparum (3k chip and 24bp barcode) (Volkman et al. Nat Genet. 2007 Jan;39(1):113-9).
• Microsatellite data for P. falciparum available through Gbrowse with link-outs to GenBank records (Su et al. Science, 1999 vol. 286 (5443) pp. 1351-3).

• Promoter Prediction:
• Prediction of transcription start sites in P. falciparum provided prepublication and available on gbrowse (Brick K, Watanabe J, and Pizzi E).

• Documentation related to data types has been improved.
• Gbrowse tracks have been organized and help associated with gbrowse items have been improved.

Plasmodium microarray resources 22 July 2008

Fourth updated snapshot of the reannotation of the P. falciparum 3D7 genome 15 July 2008

Approval for sequencing additional Plasmodium isolates and species. 11 June 2008

Third updated snapshot of the reannotation of the P. falciparum 3D7 genome 6 June 2008

An updated snapshot of the reannotation of the P. falciparum 3D7 genome 19 May 2008

The effort to systematically update the annotation for P. falciparum 3D7 genome started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Institute (WTSI) and the ApiDB team. The Wellcome Trust and Burroughs Wellcome Fund-sponsored workshop was held in Hinxton, UK and was attended by nearly 30 Plasmodium researchers contributing expertise in various aspects of Plasmodium biology, plus more than 10 bioinformatics support staff from the Artemis, GeneDB and ApiDB teams. During the workshop 2700 genes were edited using Artemis and ACT software, mainly with the addition of new or alternative functional descriptions (e.g. product names, GO terms, EC numbers and miscellaneous textual comments).

After the workshop, intensive manual reannotation of the genome has continued at WTSI with the help of several members of the community. First, the structures of more than 700 gene models have been changed and new gene models have been added. In addition, curation staff at GeneDB have reviewed all User Comments submitted to PlasmoDB. Over the coming months, the emphasis will switch to a careful genome-wide review of functional annotation.

The annotation presented here in PlasmoDB is the second snapshot of a work in progress and intended to inform you about the new annotation and elicit any feedback that you may have. Please add a User Comment to any gene about which you have additional information. This information is forwarded to the GeneDB curators on a weekly basis and will be included in the next snapshot. In order to expedite the annotation, the following are of particular value to the manual curators:

• New product names with the PubMed ID of the paper in which they were first cited,
• Additional PubMed IDs of any papers from which the function of the gene/protein can be ascribed
• EC number
• Alternative/updated gene names and aliases.
• Evidence that a gene structure has been incorrectly called. Please include a description of the evidence that you have used (e.g. full length cDNA) and the new sequence.

The ongoing reannotation is being systematically carried out by Ulrike Böhme and Bart Barrell (Wellcome Trust Sanger Institute) with extensive help from several community volunteers, in particular Chris Newbold (Oxford, UK), Tom Templeton (Cornell, US), Eric Maréchal (Grenoble, France). For the annotation, the Artemis software was redesigned by Tim Carver and changes are recorded within a Chado database (GeneDB) designed and maintained by Adrian Tivey and Chinmay Patel.

Workshop participants included

• Oliver Bilker (Imperial Coll, London)
• Serge Bonnefoy (Inst Pasteur, Paris)
• Pete Bull (Kenya Med Res Inst, Kilifi)
• Jane Carlton (New York Univ)
• Brendan Crabb (Walter & Eliza Hall Inst, Melbourne)
• Christian Doerig (Univ Glasgow)
• Malcolm Gardner (Seattle Biomedical Res Inst)
• Hagai Ginsburg (Hebrew Univ, Jerusalem)
• George Githinji (MOMS, Tanzania)
• Taco Kooij (Heidelberg Univ)
• Dominic Kwiatkowski (Oxford Univ & WTSI)
• Sue Kyes (Oxford Univ)
• Thomas Lavstsen (Copenhagen)
• Manuel Llinas (Princeton Univ)
• Eric Marechal (CNRS, Grenoble)
• Dan Milner (Harvard Univ)
• Fingani Mphande (Karolinska Inst)
• Dan Neafsey (Broad Inst)
• Chris Newbold (Oxford Univ)
• Stuart Ralph (Melbourne Univ)
• Gowthaman Ramasamy (Seattle Biomedical Res Inst)
• Robert Sinden (Imperial Coll, London)
• Worachart Sirawaraporn (Mahidol Univ, Bangkok)
• Dominique Soldati (Univ Geneva)
• Tim Stedman (MR4 / ATCC)
• Tom Templeton (Cornell Univ, New York)
• Akhil Vaidya (Drexel Univ, Philadelphia)
• Scott Westenberger (Scripps Inst, La Jolla)
• Jennifer Wortman (Univ Maryland, Baltimore)

• Andy Berry, Ulrike Boehme, Celine Carret, Tim Carver, Al Ivens, Arnab Pain, Adrian Tivey & Matt Berriman (GeneDB / Wellcome Trust Sanger Inst)
• Brian Brunk, Zhongqiang Chen, Mark Heiges, Lucia Peixoto, Dhanasekaran Shanmugam & David Roos (ApiDB / Univ Georgia & Univ Pennsylvania)

Draft Reannotation of the P. falciparum genome is now available. 1 February 2008

Workshop participants included

• Oliver Bilker (Imperial Coll, London)
• Serge Bonnefoy (Inst Pasteur, Paris)
• Pete Bull (Kenya Med Res Inst, Kilifi)
• Jane Carlton (New York Univ)
• Brendan Crabb (Walter & Eliza Hall Inst, Melbourne)
• Christian Doerig (Univ Glasgow)
• Malcolm Gardner (Seattle Biomedical Res Inst)
• Hagai Ginsburg (Hebrew Univ, Jerusalem)
• George Githinji (MOMS, Tanzania)
• Taco Kooij (Heidelberg Univ)
• Dominic Kwiatkowski (Oxford Univ & WTSI)
• Sue Kyes (Oxford Univ)
• Thomas Lavstsen (Copenhagen)
• Manuel Llinas (Princeton Univ)
• Eric Marechal (CNRS, Grenoble)
• Dan Milner (Harvard Univ)
• Fingani Mphande (Karolinska Inst)
• Dan Neafsey (Broad Inst)
• Chris Newbold (Oxford Univ)
• Stuart Ralph (Melbourne Univ)
• Gowthaman Ramasamy (Seattle Biomedical Res Inst)
• Robert Sinden (Imperial Coll, London)
• Worachart Sirawaraporn (Mahidol Univ, Bangkok)
• Dominique Soldati (Univ Geneva)
• Tim Stedman (MR4 / ATCC)
• Tom Templeton (Cornell Univ, New York)
• Akhil Vaidya (Drexel Univ, Philadelphia)
• Scott Westenberger (Scripps Inst, La Jolla)
• Jennifer Wortman (Univ Maryland, Baltimore)

• Andy Berry, Ulrike Boehme, Celine Carret, Tim Carver, Al Ivens, Arnab Pain, Adrian Tivey & Matt Berriman (GeneDB / Wellcome Trust Sanger Inst)
• Brian Brunk, Zhongqiang Chen, Mark Heiges, Lucia Peixoto, Dhanasekaran Shanmugam & David Roos (ApiDB / Univ Georgia & Univ Pennsylvania)

PlasmoDB 5.4 is released 31 October 2007

• A slightly modified reference genome for P. falciparum (several gaps have been closed on chr10 & 11).
• P. berghei gametocyte proteomics data (Khan et al, Cell 121:675-87).
• Many additional P. falciparum SNPs (unpublished data from the Broad Inst).
• Additional ESTs (Watanabe et al, Nucl Acids Res 32:D334-8; Lu et al, BMC Genomics 8:255; Florent et al, Mol.Biochem.Parasitol. 135:143-8)
• Expression profiling data for antigenic and adherent variants of P. falciparum 3D7 (Mok et al, Molec Biochem Parasitol 151:184-92).
• User comments submitted prior to June 2007 have now been incorporated into the official annotation.
• Sequence assemblies for 11 falciparum strains from the Broad Institute have just been released and are available on the PlasmoDB download site.

• Faster loading of Gene and Genome Browser pages.
• Improved synteny views in the Genome Browser.
• Browser views of rodent malaria genomes colored to indicate chromosomes (Kooij et al, PLoS Pathog 1:e44).
• Gene page links to various external data sources (including PlasmoMAP, TDRtargets, UCSC P. falciparum genome browser, Ontology-based Pattern Identification and literature databases).
• More convenient access to help ... please click the "Ask us a Question" link on the left of every page, or the "Contact Us" at bottom to report problems or suggest improvements to the database.

• Naming, e.g. "Apical membrane antigen 1 is also known as AMA1, AMA-1, Pf83, Rhoptry Membrane Antigen, RMA1" or "this gene is now recognizable as XXX based on Pfam domain ###."
• Gene models, e.g. "Corrected cDNA sequence for gene XXX: <sequence>, based on RACE and primer extension for 5' UTR and polyA-tailed cDNA clone for 3' UTR" or "RT-PCR confirms annotated CDS sequence as correct." Note that confirmation of existing annotation can be as valuable as corrections!
• Function, e.g. "Enzymatic activity for gene XXX has been confirmed" or "Protein XXX is predicted to target to the apicoplast, but an epitope-tagged construct shows cytoplasmic localization." Be sure to provide name and/or PubMedID if available.

Tutorials offered now for more platforms 7 October 2007

PlasmoDB 5.3 is released 19 June 2007

The PlasmoDB 5.3 web site also has significant improvements to the query and results pages. Many of the queries have been reorganized. For example, the Predicted Functional Interaction query now allows input of a list of genes and a clearer explanation of what to get from the query (e.g., find high confidence predicted interactions between members of the input gene list). The results from this and all queries can be sorted. It is also now possible to add columns of interest (e.g., protein features, GO annotation, even expression characteristics) and sort on them.

New data and queries in PlasmoDB 5.3:

• Genome sequence and annotation for Plasmodium knowlesi from the Wellcome Trust Sanger Institute Pathogen Sequencing Unit. P. knowlesi is included in many of the queries to identify genes, genomics sequences, ESTs, and ORFs by various features.
• Microarray studies have been incorporated from a series of 3 papers on gene silencing (Duraisingh et al. Cell 2005) and invasion pathways (Baum et al. PLoS Pathogens 2005; Stubbs et al. Science 2005) in P. falciparum.
• A microarray study in P. berghei from a paper on translational repression in gametocytes (Mair et al. Science 2006).
• A refined mapping of epitopes to Plasmodium provided by the Immune Epitope Database and Analysis Resource. A query is now provided to identify genes whose encoding protein has an epitope at different levels of confidence.
• Updated E.C. number and metabolic pathway assignments, Interpro protein domains and associated GO predictions, MR4 reagent links, homologies to entries in the NRDB protein database and links to structures in PDB.
• A new build of ortholog groups from Orthomcl for use in PlasmoDB. The list of genomes represented has increased from 55 to 87 and includes all the organisms covered by the different NIH/NIAID funded Bioinformatics Resource Centers.

New features in PlasmoDB 5.3:

• Most of the queries have been reorganized to make them more intuitive. Some include a new "Advanced Parameters" section. See for example "Identify Genes based on EST evidence."
• The columns displayed in query result pages are improved. The result pages also offer options for sorting, adding new columns, and moving columns around.
• Downloading results is improved. A choice of formats is provided including tab-delimited, text, GFF, and FASTA to meet different needs.
  • Tab delimited provides an expanded list of annotations that can be directly exported as an Excel spreadsheet.
  • Text provides a detailed summary for each gene including SNPs, Y2H interactions, metabolic pathways, MR4 reagents, protein structures, notes, sequence, and many other choices.
  • GFF is a format recognized by many applications such as the genome browser, gbrowse.
  • FASTA also provides a common format used for BLAST and other applications. The FASTA option provides the functionality of the SRT (sequence retrieval tool) found in earlier versions of PlasmoDB.

PFGRC offers course on Microarray Tech., April 2007 14 February 2007

The NIAID sponsored Pathogen Functional Genomics Resource Center at TIGR announces that it will conduct a four day course titled, "Introduction to Microarray Technology." The workshop will be held on the TIGR campus on April 16-19, 2007. The course will provide an overview of the two-dye spotted microarray platform. The course is designed for hands on participation and attendees will actively learn to make the most of their microarrays through a combination of wet lab and bioinformatics sessions.

The wet lab portion will be taught by PFGRC staff who are directly involved in microarray production. Participants will be guided through probe preparation and hybridization protocols. The training will also consist of detailed discussions on dye coupling, slide pre-hybridization, hybridization, and scanning techniques. Other topics for discussion will include the importance of assessing source material and probe quality, comparisons of various slide surfaces, and printing techniques.

The bioinformatics portion of the course covers an introduction to the stages of microarray data analysis. Major topics include data management, image analysis, normalization, and data mining. Fundamental data analysis concepts will be taught using a mix of lectures and interactive hands-on sessions. Participants will analyze the microarrays they prepared, using the open-source TM4 software suite while working closely with the software developers. CDs containing microarray datasets and the TM4 suite will be provided.

The course will be provided free of charge. Attendees will be responsible for their travel and lodging. This introductory course is one of several offered by the PFGRC on variety of functional genomics topics. Attendance will be limited to 14 participants.

Interested participants will find the preliminary course agenda here, and registration information here.

ApiDB Workshop, June 3-6, 2007 5 December 2006

The workshop will be a 3.5 day introduction to apicomplexan database resources that are part of the ApiDB Bioinformatics Resource Center ( ApiDB.org, PlasmoDB, ToxoDB, and CryptoDB ).

The application deadline is January 19, 2007 (Application). Please click here for further information and to register.

PlasmoDB 5.2 is released 17 November 2006

The PlasmoDB 5.2 site also includes new features such as allowing you to keep your Query History for later use, an improved keyword search and a significantly upgraded Query & Tools page.

New data and queries in PlasmoDB 5.2:

• Array data from Kidgell et al. PLoS Pathogens 2006 A systematic map of genetic variation in Plasmodium falciparum.
• Polymorphism data based on resequencing and array analyses.
  • SNPs generated by the NIH: Based on CDS sequences from strains 3D7, 7G8, D10, Dd2, HB3 (kindly provided in advance of publication by X. Su; reference: J. Mu et al, Nature Genetics, in press)
  • SNPs generated by the Broad Institute: Based on whole genome sequence for strains Dd2 and HB3, and partial genome sequence for multiple strains (kindly provided in advance of publication by D. Decaprio, S.K. Volkman & D.F. Wirth; reference: S.K. Volkman et al, Nature Genetics, in press)
  • SNPs generated by the WTSI: Based on whole genome sequence for strains Ghana1 and IT and a comparison with P. reichenowi (kindly provided in advance of publication by D.C. Jeffares & M. Berriman; reference: D.C. Jeffares et al, Nature Genetics, in press).
  • Array CGH data on a variety of Plasmodium strains kindly provided by E. Winzeler.
• A query to generate gene lists based on SNP characteristics such as non-synonymous / synonymous substitutions and SNP density.
• Plasmodium ESTs from the Oct. 2, 2006 release of dbEST.
• Interproscan analysis of Plasmodium proteins.
• PlasmoCyc pathways, available from gene pages

• Save past searches (Persistent Query History)
• Reorganized Query and Tools page
• Improved text search
• New tutorial movies

• Gametocyte data from Young et al. Mol Biochem parasitol 2005.
• Expression profile similarity for erythrocytic stage data from P. falciparum 3D7, HB3, and DD2 (Llinas et al., Nucl. Acids. Res. 2006; Bozdech et al PLos Biol 2003). New to 5.2 is the inclusion of P. berghei data (Hall et al. Science 2005).

PlasmoDB 5.1 is released 16 August 2006

• Rodent malaria parasite (RMP) data
  • For P. berghei and P. chabaudi
    • Genome Browser tracks showing synteny to P. falciparum
    • TIGR Gene Index (TGI) tracks in the Genome Browser
    • Pfam domains mapped to predicted protein products
  • A Genome Browser track showing glass slide array oligos mapped to P. yoelii
• Updated mappings from PlasmoDB genes to
  • The Protein Data Bank (PDB)
  • Genbank, RefSeq and Swissprot
  • Reagents from the MR4 Consortium
• tRNA gene predictions for P. vivax, P. berghei, P. chabaudi and P. yoelii.
• Migrated functionality PlasmoDB 4.4
  • Array element pages that describe the details of oligos and their expression.
  • A protein secondary structure query and track on the gene page
  • Links from PlasmoDB genes to predicted protein structure models
  • The "Add a Comment" facility (for commenting on genes and chromosomes/contigs).
  • A newly designed User Login process. (In upcoming releases logging in to the site will let you store your query history and set preferences. For now, it just lets you Add a Comment).
• Genome Browser features
  • Save your favorite track configurations and regions of interest.
  • Download the sequence of any feature in any track
• Improved citations on the Data Sources page
• Behind the scenes, a new issue tracking system so we can better respond to your support issues.

PlasmoDB 5.0 is fully released (PlasmoDB 4.4 still available) 25 May 2006

PlasmoDB 5.0 implements significant 'under-the-hood' changes, making it much easier to generate future releases in short cycles. In addition, these changes to ensure a consistent look for all ApiDB projects, including PlasmoDB, CryptoDB, and ToxoDB (supported by a Bioinformatics Resource Center contract from the US NIH / NIAID).

Because it will take some time to implement all of the PlasmoDB 4.4 functionality in the new architecture, PlasmoDB 4.4 remains active, and the results of queries run under it may be exported to PlasmoDB 5.0 (see PlasmoDB 4.4 Query History).

New Data in PlasmoDB 5.0 (relative to version 4.4) include:

• the complete genome sequence for P. vivax Salvador, along with a complete set of annotated gene models
• the complete genome sequence for P. berghei, along with a complete set of annotated gene models
• the complete genome sequence for P. chabaudi, along with a complete set of annotated gene models
• TIGR Gene Indices for P. vivax, P. falciparum, and P. yoelii
• protein-protein interaction data, based on a genome-wide yeast 2-hybrid analysis (LaCount et al. Nature 438:103; 2005)
• new ortholog analyses, using the OrthoMCL algorithm to group genes from several Plasmodium species with other complete eukaryotic and prokaryotic genomes (Chen et al., Nucl. Acids Res. 34:D363; 2006)
• Computational predictions for functional interactions in P. falciparum from the PlasmoMAP project are provided based on co-evolution and co-expression of genes (Date & Stoeckert Genome Res. 16:542; 2006). This data is now available as a PlasmoDB query.
• Updated mappings for pathways and Enzyme Classifications (EC).

New Features in PlasmoDB 5.0 Include:

• an interactive genome browser, based on the GBrowse module of the GMOD project
• syntenic relationships between P. falciparum, P. vivax, and P. yoelii (Carlton et al., Nature 419:512; 2002).

Finally, we are pleased to report a new CD-ROM version of the Plasmodium Genome Database. PlasmoCD provides users lacking reliable high-speed internet connections with full access to the complete genomes of P. falciparum, P. vivax, and P. yoelii, along with gene models, annotation, BLAST hits, ortholog results, expression data, and search functions for querying and integrating these results across species.

P. berghei and P. chabaudi genomes added 4 April 2006

PlasmoMAP data included 4 April 2006

PlasmoDB 5.0 Beta announced 1 February 2006

PlasmoDB 5.0 Beta released 9 December 2005

PlasmoDB 5.0 Beta features:

• A new interactive genome browser, based on the GBrowse module of the GMOD project, providing rapid visualization of the parasite genome and gene models, custom restriction site identification, open reading frame identification, and downloads in various formats.
• The complete genome sequence for P. vivax Salvador, along with a complete set of annotated gene models, and syntenic relationships between P. falciparum, P. vivax, and P. yoelii (from Jane Carlton, TIGR).
• Updated P. falciparum annotation, including curated literature citations; updated GO term curation from Andy Berry, Matt Berriman, and the Sanger curation effort; updated EC/pathway mappings from Hagai Ginsburg.
• TIGR Gene Indices for P. vivax, P. falciparum, and P.yoelii.
• Corrected expression profiles from glass-slide arrays for P. falciparum 3D7, HB3 & Dd2 (from Manuel Llinas, Zybnek Bozdech & Joe DeRisi).
• Updated structural data, including information from the structural genomics consortia.
• Protein-protein interaction data for P. falciparum, based on a genome-wide yeast 2-hybrid analysis (LaCount et al. Nature 438:103; 2005).
• New ortholog analyses, using the OrthoMCL algorithm to group genes from several Plasmodium species with other complete eukaryotic and prokaryotic genomes (Chen et al. Nucl Acids Res, in press).

Finally, we are pleased to report a new CD-ROM version of the Plasmodium Genome Database. PlasmoCD provides users lacking reliable high-speed internet connections with full access to the complete genomes of P. falciparum, P. vivax, and P. yoelii, along with gene models, annotation, BLAST hits, ortholog results, expression data, and search functions for querying and integrating these results across species. PlasmoCD 4.1 can be downloaded from the PlasmoDB web site, or requested by sending e-mail to <help@PlasmoDB.org>.

GBrowse added to PlasmoDB 9 December 2005

• Custom restriction site identification
• Open reading frame identification
• Custom downloads in various formats:
  • FASTA
  • GFF (2)
  • GFF3
  • BSML (XML)
  • EMBL
  • GenBank
  • GAME
  • GCG

PlasmoDB 5.0 Beta uses GUS 3.5 and the WDK 9 December 2005

OrthoMCL orthologous groups have been updated. 9 December 2005

Yeast Two-hybrid protein interaction data for P. falciparum 9 December 2005

Intraerythocytic expression profiles have been recalculated 15 September 2005

Raw data were loess normalized using the default loess implementation in the R package for microarray analysis (marray). The non-background corrected foreground mean was used as input to the loess algorithm. Replicate arrays for the same time point were then averaged to give one value for each timepoint/gene. Data was then smoothed using a least squares fit to each data point and its two neighbors on each side.

The profiles seen in PlasmoDB 4.4 have also been corrected. The correlation table that gives correlations between the different studies (the three DeRisi and the two Winzeler) has been recalculated based on the new profiles. This new data is not yet displayed on 4.4 but will be on 5.0 Beta.