Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher's Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies.
[Tool] name: g:Profiler url: http://biit.cs.ut.ee/gprofiler is_online_tool: true developer: http://www.ut.ee/ "University of Tartu" country-name: Estonia publication: PMID:17478515 license: free description:g:Profiler is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology, pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are: g:Convert for converting between different database identifiers; g:Orth for finding orthologous genes from other species; and g:Sorter for searching a large body of public gene expression data for co-expression. g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs.
[Tool] name: GeneTools url: http://www.genetools.microarray.ntnu.no/common/intro.php is_online_tool: true developer: http://www.ntnu.no/ "Norwegian University of Science and Technology" developer: http://www.microarray.no/ "Norwegian Microarray Consortium" license: free description:GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0 (explore Gene Ontology). The NMC Annotation Database V2.0 provides information from UniGene, EntrezGene, SwissProt and Gene Ontology (GO).
Major features are:
GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match.
[Tool] name: GoAnnotator url: http://xldb.fc.ul.pt/rebil/tools/goa/ is_online_tool: true developer: http://xldb.fc.ul.pt/ "XLDB Group, Faculdade de Ciências da Universidade de Lisboa" publication: PMID:15719064 license: free description:GoAnnotator is a tool for verification of electronic protein annotations using GO terms automatically extracted from literature.
[Tool] name: GOCat url: http://eagl.unige.ch/GOCat/ is_online_tool: true developer: http://www.natlang.hcuge.ch/ "Text Mining group, University of Geneva" developer: http://www.isb-sib.ch/groups/Swiss-Prot.htm "Swiss-Prot group, Swiss Institute of Bioinformatics" publication: PMID:16287934 publication: PMID:15960836 license: free description:The Gene Ontology Categorizer (GOCat)[external website] is an automatic text categorizer. The tool classifies any input text (a few words, an abstract, a set of PubMed Identifiers...) into Gene Ontology categories. The system, originally developed for the first BioCreative evaluation campaign, aims at facilitating functional annotation of gene and gene products using text mining methods. For every predicted category, a confidence score and a short text passage, extracted from the input text, are provided. The interface can also be used to navigate the Gene Ontology thanks to direct Quick GO links.
[Tool] name: GoFigure url: http://udgenome.ags.udel.edu/gofigure/ is_online_tool: true developer: http://www.udel.edu/ "University of Delaware" publication: PMID:14668239 license: free description:GoFigure is a web accessible tool that uses BLAST to predict Gene Ontology annotation by identifying annotated homologs of an unknown query sequence. Either DNA or protein sequences can be submitted, and multiple queries can be done by submitting a file containing FASTA formated sequences. Results are retrieved by email and may be viewed as either graphs or a tab delimited file. Results can also bedownloaded as a tar file.