infection is typically asymptomatic in healthy individuals , but may lead to congenital birth defects and encephalitis in immuno - suppressed individuals ( 1,2 ) . toxodb , initially released in may 2001 , has been substantially updated in both content and functionality since last described in january 2003 ( 3 ) . toxodb provides access to the genome sequence and annotation of the t. gondii me49 strain . the parasite genome is 63 mb in size and consists of 14 chromosomes ( 4 ) . the initial toxodb release was not supported by a relational database and thus the site had restricted functionality and little capability to integrate diverse data types such as gene expression data and single nucleotide polymorphism data ( snps ) with genomic sequence . since initial publication , toxodb has been completely rebuilt using a common architecture similar to another apicomplexan database project , plasmodb ( 5 ) . both sites , along with cryptodb , are component sites of apidb , the apicomplexan bioinformatics resource center ( 6 ) . many of the new methods of data loading , querying and presentation that are mentioned here have been applied to all of the apidb sites to provide a common research platform and facilitate data access among this group of related organisms . apidb ( http://apidb.org/ ) serves as an  umbrella site for cross - species comparisons . researchers can mine for toxoplasma genes at apidb directly or via their orthologous relationship(s ) to genes in other apicomplexan species . toxodb provides access to the genome sequence and annotation of t. gondii ( me49 strain ) and the genomic sequence of the gt1 , veg and rh ( chr ia and chr ib ) strains . the current database version ( release 4.2 ) also contains manual annotation ( solicited in the initial genome annotation and entered by users as user comments ) , ests , tigr gene indices clustered ests , sage tags , snps , cosmid and bac ends , microarray and proteomics studies , all of which have been mapped to the genome ( 7,8 ) . the database contains the results of automated analyses including gene predictions ( using various algorithms ) , open reading frames ( orfs ) greater than 50 aa and protein feature predictions [ signal peptides , transmembrane domains , hydrophobicity plots , aa content and interpro domains ( 9 ) ] , gene ontology function predictions , and blast similarities to the ncbi non - redundant protein database ( table 1 ) . table 1.data and analyses that have been integrated into toxodb and the number of genes that are impacteddata typedata sourcenumber of genesgenestigr8032community annotationvarious contributors1610orthologsgenerated from orthomcl4616go termstigr ; interpro3136ec numberstigr800snpsjohn boothroyd laboratory ; david roos laboratory7322microarraydavid roos laboratory7664estsdbest , tigr gene indices6080sage tagstgsagedb ( 14)6284proteomicsjohnathan wastling laboratory ; john murray laboratory2435epitopesiedb10metabolic pathwayskegg pathway614 data and analyses that have been integrated into toxodb and the number of genes that are impacted in addition , we have used the orthomcl algorithm to group genes from t. gondii with orthologous genes from 86 other eukaryotic and prokaryotic genomes ( 10 ) . a mapping of immune epitopes identified in toxoplasma provided by the immune epitope database and analysis resource ( iedb ) ( 11 ) has been integrated . affymetrix probes mapped to the genome are visible in gbrowse , as are snps generated from nucmer alignments of sequences from the gt1 , veg and rh ( chr ia and ib ) strains against the reference me49 sequence . users gain access to these new data types in record pages and by queries using the powerful query interface ( see data - mining section ) . as a part of the complete restructure of the toxodb resource , the practice of using flat files as a means of data storage we now use gus 3.5 , and load data into an underlying oracle database in a systematic fashion . gus ( genomics unified schema ) is an open source project ( www.gusdb.org ) with a rich relational schema including sequence annotation , expression data and proteomics using controlled vocabularies and ontologies ( 12 ) . toxodb also employs the gus wdk ( web development kit , www.gusdb.org/wdk ) , to access the database from the internet dramatically improving the way the website operates . this transformation has added considerable increased functionality for database users and conforms to the model used by all apidb projects , making it possible for us to generate future database releases in short cycles . toxodb provides access to the genome sequence and annotation of t. gondii ( me49 strain ) and the genomic sequence of the gt1 , veg and rh ( chr ia and chr ib ) strains . the current database version ( release 4.2 ) also contains manual annotation ( solicited in the initial genome annotation and entered by users as user comments ) , ests , tigr gene indices clustered ests , sage tags , snps , cosmid and bac ends , microarray and proteomics studies , all of which have been mapped to the genome ( 7,8 ) . the database contains the results of automated analyses including gene predictions ( using various algorithms ) , open reading frames ( orfs ) greater than 50 aa and protein feature predictions [ signal peptides , transmembrane domains , hydrophobicity plots , aa content and interpro domains ( 9 ) ] , gene ontology function predictions , and blast similarities to the ncbi non - redundant protein database ( table 1 ) . table 1.data and analyses that have been integrated into toxodb and the number of genes that are impacteddata typedata sourcenumber of genesgenestigr8032community annotationvarious contributors1610orthologsgenerated from orthomcl4616go termstigr ; interpro3136ec numberstigr800snpsjohn boothroyd laboratory ; david roos laboratory7322microarraydavid roos laboratory7664estsdbest , tigr gene indices6080sage tagstgsagedb ( 14)6284proteomicsjohnathan wastling laboratory ; john murray laboratory2435epitopesiedb10metabolic pathwayskegg pathway614 data and analyses that have been integrated into toxodb and the number of genes that are impacted in addition , we have used the orthomcl algorithm to group genes from t. gondii with orthologous genes from 86 other eukaryotic and prokaryotic genomes ( 10 ) . a mapping of immune epitopes identified in toxoplasma provided by the immune epitope database and analysis resource ( iedb ) ( 11 ) has been integrated . affymetrix probes mapped to the genome are visible in gbrowse , as are snps generated from nucmer alignments of sequences from the gt1 , veg and rh ( chr ia and ib ) strains against the reference me49 sequence . users gain access to these new data types in record pages and by queries using the powerful query interface ( see data - mining section ) . as a part of the complete restructure of the toxodb resource , the practice of using flat files as a means of data storage was abandoned in early 2006 . we now use gus 3.5 , and load data into an underlying oracle database in a systematic fashion . gus ( genomics unified schema ) is an open source project ( www.gusdb.org ) with a rich relational schema including sequence annotation , expression data and proteomics using controlled vocabularies and ontologies ( 12 ) . toxodb also employs the gus wdk ( web development kit , www.gusdb.org/wdk ) , to access the database from the internet dramatically improving the way the website operates . this transformation has added considerable increased functionality for database users and conforms to the model used by all apidb projects , making it possible for us to generate future database releases in short cycles . toxodb currently provides 40 different queries of the data and several ancillary tools for analyzing , retrieving or viewing the data such as blast , pathway tools and an installation of the gmod project genome browser ( 13 ) . the toxodb  query & tools page has been restructured to make all queries available at a glance . most of the individual queries have been reorganized into categories such as  position , for example , the toxodb keyword search has been significantly improved , offering the user control over which fields in the database are searched , including the official annotation , synonyms , user - supplied comments , domain names , blast similarities , etc . many queries , such as  find snps based on gene id , now allow a gene i d list as input [ either typed ( or copied ) by hand or uploaded from a file ] facilitating analyses on large groups of genes . the results from all queries can be sorted based on various criteria ( columns in the returned data set ) and users can also add additional criteria for display ( e.g. add columns to display protein features , go annotation , expression characteristics for gene results , etc . ) and sort on them as well . once the appropriate selection of data types to display has been achieved , users can integrate these search results with other search results using the  query history page , or the data can be downloaded in multiple formats for further analysis by the researcher ( figure 1 ) . figure 1.screenshots showing the flow of a query in toxodb . from the query & tools page , users can go to particular queries for expression evidence ( est or mass spec evidence ) , to the results page where they can sort , manage ( add or delete ) columns of data and open gene pages . the query history page permits users to manipulate previous queries including combining them and/or downloading the resulting data . individual genes are listed on the gene results page and each gene has its own gene page , illustrated here by the gene encoding elongation factor 1-alpha . the gene page summarizes all information that is available for a gene including gene model predictions , snps , blast similarities , protein domains , ests , proteomic evidence of expression and microarray expression analyses . screenshots showing the flow of a query in toxodb . from the query & tools page , users can go to particular queries for expression evidence ( est or mass spec evidence ) , to the results page where they can sort , manage ( add or delete ) columns of data and open gene pages . the query history page permits users to manipulate previous queries including combining them and/or downloading the resulting data . individual genes are listed on the gene results page and each gene has its own gene page , illustrated here by the gene encoding elongation factor 1-alpha . the gene page summarizes all information that is available for a gene including gene model predictions , snps , blast similarities , protein domains , ests , proteomic evidence of expression and microarray expression analyses . toxodb uses the gbrowse genome browser ( www.gmod.org ) ( 13 ) to display gene models , est alignments , snps , sage tags , etc . gbrowse enables visualization of the parasite genome and gene models , custom restriction - site identification , open reading frame identification , and facilitates download of data in various formats . all genome sequences [ me49 , gt1 , veg and rh ( chr ia , ib ) ] are also available in blast - searchable databases and for download in fasta , genbank and embl formats . toxodb users may now register and log in to the site . doing so enables a researcher to add comments to genes and genomic sequences . queries in the query history page can be organized ( re - named or deleted ) as well as combined with other results ( figure 1 ) . this is a very powerful feature that allows users to refine their results so that precise sets of genes can be discovered . it supports summary reports ( excel compatible tab delimited text ) , gff , fasta and a detailed report that includes almost all available data for each gene in the users result table . use of this facility as well as many others on the site are now described in short video tutorials that are accessible from the database home page . the last two years were spent on major infrastructure and design elements for toxodb . our future growth will be in the area of increased data acquisition and integration with existing and future data sets . specifically , we are planning to load and integrate many expression data sets ( rna expression and protein expression ) that are just becoming available . we also expect to load and integrate other array - based data sets such as chip on chip and array cgh . as new data are added , we will be adding additional queries and tools to view these data . an area of significant future development will be improving the ability of users to compare the various different sequenced parasite strains visually and download sequence alignments between them .
toxodb ( http://toxodb.org ) is a genome and functional genomic database for the protozoan parasite toxoplasma gondii . 
 it incorporates the sequence and annotation of the t. gondii me49 strain , as well as genome sequences for the gt1 , veg and rh ( chr ia , chr ib ) strains . 
 sequence information is integrated with various other genomic - scale data , including community annotation , ests , gene expression and proteomics data . 
 toxodb has matured significantly since its initial release . here 
 we outline the numerous updates with respect to the data and increased functionality available on the website .