from Sabeeha Merchant and Matteo Pellegrini
We have developed a functional annotation tool for Chlamydomonas, which is a resource to visualize pathway maps, identify enriched biological terms or convert Chlamydomonas reinhardtii gene identifiers. Please visit http://pathways.mcdb.ucla.edu/chlamy/ to use this tool.
We have also mapped the ~ 5 million-plus EST reads from JGI-UCLA and Genoscope (see 23 June post below) to the version 3 browser because of some interest in using the previous version of the assembly. The alignment can be viewed by following appropriate links at http://genomes.mcdb.ucla.edu/.
The Algal Functional Annotation Tool
This is a web-based tool that uses lists of protein identifiers (such as Chlamydomonas JGI protein IDs and Augustus model IDs) and searches the entire list against a comprehensive list of annotation databases to elucidate enriched (and therefore interesting) biological functions/processes within the given gene list.
This tool aims to eliminate the need to manually search these individual databases on a gene-by-gene basis to reveal underlying biological themes. These databases have been parsed and pre-processed to optimize this process from the point of view of the end-user.
The databases currently included are:
- – KEGG Pathways (Kyoto Encyclopedia of Genes and Genomes)
- – Panther Pathways
- – MetaCyc (Encyclopedia of Metabolic Pathways)
- – Reactome Pathways
- – Gene Ontology (GO)
- – MapMan Ontology
- – KOG (Eukaryotic Clusters of Orthologous Groups)
- – Pfam (PfamA and Pfam Clans)
- – Interpro
For some databases, such as GO and MapMan, in addition to searching against the Chlamydomonas annotation, terms inferred from Arabidopsis homology are also searched against. KEGG pathways may also be dynamically visualized using the proteins in the given gene list.
Subsets of enrichment may be re-run through the tool and in most cases the results data may be downloaded as a tab-delimited text file.
The tool may be accessed directly at http://pathways.mcdb.ucla.edu/chlamy/ .
Examples of use and a sample gene list are included to explore the tool.
Feedback about the tool (including requests for other databases/features you’d like to see) may be directed at firstname.lastname@example.org