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ToxoDB: an integrated Toxoplasma gondii database resource.

Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ, Wang H, Brunk BP - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA.

ABSTRACT
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.

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Related in: MedlinePlus

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.
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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.

Mentions: 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’, ‘Expression’ and ‘Function’ to make them more intuitive to the average researcher. Enhanced functionality for the queries has also been added. 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 ID 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.


ToxoDB: an integrated Toxoplasma gondii database resource.

Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ, Wang H, Brunk BP - Nucleic Acids Res. (2007)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238934&req=5

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.
Mentions: 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’, ‘Expression’ and ‘Function’ to make them more intuitive to the average researcher. Enhanced functionality for the queries has also been added. 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 ID 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.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus