GCP Comparative Stress Gene Catalogue

The central objective of the Dayhoff GCP Comparative Stress Gene Catalog is to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresse such as water deficit (“drought”). The comparative stress gene catalog Dayhoff is a compendium of protein families, phylogenetic trees, multiple sequence alignments, and associated experimental evidence related to abiotic stress-responsive genes in plants. The Dayhoff stress gene catalog desktop is accessible either by selection of one of the icons, which are linked to main features in the databases, or by selecting database features from the start menu on the left.
There are three main options for using the database: by browsing stress protein families, by querying database by gene names or protein names, and by BLAST searching against protein families.

Browsing protein families: selections can be made at choice with the List all Stress Protein Family option. A list of protein families as well as links for phylogenetic trees and multiple sequence alignments (MSA) will be shown.

Protein family information: this selection provides information of the selected family and of the compiled stress protein used.
More details of all members of proteins in the selected family will be shown just by clicking. A list of Uniprot IDs, protein names and gene locus identifier is provided. Clicking on the Uniprot ID link will lead to the Uniprot database ( http://pir.georgetown.edu) .

From the page "Get Candidate Stress Proteins" a list of candidate stress proteins, containing in the selected protein family, can be displayed. The results can be refined by adjusting the provided parameters, i.e. minimum identity, minimum E-value, minimum score. The information of related-stress and experimental resources, Blast statistics, and some other information are also provided.

By the same token, the user may find the metabolic pathway(s) associated to this protein family by clicking the button “ Get KEGG Metabolic Pathway”. Link(s) in the KEGG Pathway ID column will directly link to the KEGG database. The enzyme(s) in the KEGG pathway associated with the selected stress protein family is highlighted.

The database also provides an option for mapping stress proteins in the family to some cross reference databases, i.e. the Rice Annotation Project, the Arabidopsis Information Resources and the TIGR Rice Genome Annotation. Simply selects the desired database and click “Get Mapping IDs” button.

By clicking the phylogeny button, phylogenetic trees will be shown in a ATV java webstart. The annotation information, i.e. node data, protein information, publication, multiple sequence alignments, and other general options of ATV viewer, can be viewed for each node in the phylogenetic tree by right-clicking on the node and then selecting the desired information from the menu.
The display of the phylogenetic tree can be modified at choice.
Some hands-on experience with the ATV viewer might be necessary for using this tool.

Multiple sequence alignments of all proteins in the family will be shown in Jalview webstart (experience recommended).
Database query: in the current version of the Dayhoff comparative stress gene catalog, the database can be searched by the keywords: Family name and Protein name. Users can view more information through the family id link as well as MSA and tree links. By searching Protein name, matched protein(s) will be listed together with Family id link and some other information.

BLAST protein families: protein or DNA sequence in FASTA format can be submitted for a BLAST search of the Dayhoff database as well as the GreenPhyl database. The Dayhoff comparative stress gene catalog database is interconnected to the GreenPhyl database. The resulting of best hits from both Dayhoff and GreenPhyl are displayed. These will be provided with links to Dayhoff protein families and hyperlinks to classified families at the GreenPhyl web site.

Dayhoff comparative stress gene catalog webservice

reference: Wanchana S, Thongjuea S, Ulat VJ, Anacleto M, Mauleon R, Conte M, Rouard M, Ruiz M, Krishnamurthy N, Sjolander K, van Hintum T and Bruskiewich RM (2007).
The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Research; doi: 10.1093/nar/gkm798 –  Full version ( PDF)

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