Detecting biological network organization and functional gene orthologs.
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ABSTRACT: Summary
We developed a package TripletSearch to compute relationships within triplets of genes based on Roundup, an orthologous gene database containing >1500 genomes. These relationships, derived from the coevolution of genes, provide valuable information in the detection of biological network organization from the local to the system level, in the inference of protein functions and in the identification of functional orthologs. To run the computation, users need to provide the GI IDs of the genes of interest.Availability
http://wall.hms.harvard.edu/sites/default/files/tripletSearch.tar.gzContact
dpwall@hms.harvard.eduSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Cui J
PROVIDER: S-EPMC3187654 | biostudies-literature | 2011 Oct
REPOSITORIES: biostudies-literature
Publications
Detecting biological network organization and functional gene orthologs.
Cui Jike J DeLuca Todd F TF Jung Jae-Yoon JY Wall Dennis P DP
Bioinformatics (Oxford, England) 20110819 20
<h4>Summary</h4>We developed a package TripletSearch to compute relationships within triplets of genes based on Roundup, an orthologous gene database containing >1500 genomes. These relationships, derived from the coevolution of genes, provide valuable information in the detection of biological network organization from the local to the system level, in the inference of protein functions and in the identification of functional orthologs. To run the computation, users need to provide the GI IDs o ...[more]
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