YeastWeb: a workset-centric web resource for gene family analysis in yeast.

BMC Genomics
Yanhui ChuXiudong Jin

Abstract

Currently, a number of yeast genomes with different physiological features have been sequenced and annotated, which provides invaluable information to investigate yeast genetics, evolutionary mechanism, structure and function of gene families. YeastWeb is a novel database created to provide access to gene families derived from the available yeast genomes by assigning the genes into putative families. It has many useful features that complement existing databases, such as SGD, CYGD and Génolevures: 1) Detailed computational annotation was conducted with each entry with InterProScan, EMBOSS and functional/pathway databases, such as GO, COG and KEGG; 2) A well established user-friendly environment was created to allow users to retrieve the annotated genes and gene families using functional classification browser, keyword search or similarity-based search; 3) Workset offers users many powerful functions to manage the retrieved data efficiently, associate the individual items easily and save the intermediate results conveniently; 4) A series of comparative genomics and molecular evolution analysis tools are neatly implemented to allow users to view multiple sequence alignments and phylogenetic tree of gene families. At present, Yeas...Continue Reading

References

Apr 13, 2001·Bioinformatics·C M Zmasek, S R Eddy
Nov 9, 2002·Bioinformatics·Kevin HoweRichard Durbin
Jul 31, 2003·Nucleic Acids Research·Anton J EnrightChristos A Ouzounis
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Oct 20, 2007·Nucleic Acids Research·Jongsun ParkYong-Hwan Lee

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Software Mentioned

Linux
MySQL
BLASTX
InterProScan
Perl
Génolevures
CYGD
BioPerl
Opera
Jalview Runtime Environment ( JRE

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