Gene functional similarity search tool (GFSST)

BMC Bioinformatics
Peisen ZhangKenneth Buetow

Abstract

With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and their products have been discovered and their functions have begun to be understood. Increasing amounts of data about genes, gene products and their functions have been stored in databases. To facilitate selection of candidate genes for gene-disease research, genetic association studies, biomarker and drug target selection, and animal models of human diseases, it is essential to have search engines that can retrieve genes by their functions from proteome databases. In recent years, the development of Gene Ontology (GO) has established structured, controlled vocabularies describing gene functions, which makes it possible to develop novel tools to search genes by functional similarity. By using a statistical model to measure the functional similarity of genes based on the Gene Ontology directed acyclic graph, we developed a novel Gene Functional Similarity Search Tool (GFSST) to identify genes with related functions from annotated proteome databases. This search engine lets users design their search targets by gene functions. ...Continue Reading

References

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Citations

Feb 1, 2011·Briefings in Bioinformatics·Léon-Charles TrancheventYves Moreau
Oct 13, 2007·Nucleic Acids Research·Andreas Schlicker, Mario Albrecht
Jan 29, 2008·BMC Bioinformatics·Angela del PozoAlfonso Valencia
Mar 10, 2007·Genome Biology·Andreas SchlickerFrancisco S Domingues
Nov 14, 2007·International Journal of Biological Sciences·Mengjin Zhu, Shuhong Zhao
Oct 1, 2013·BioMed Research International·Gaston K Mazandu, Nicola J Mulder
Jun 6, 2012·Advances in Bioinformatics·Gaston K Mazandu, Nicola J Mulder
Oct 20, 2015·Bioinformatics·Gaston K MazanduNicola J Mulder
Jul 31, 2016·Briefings in Bioinformatics·Gaston K MazanduNicola J Mulder
Sep 27, 2013·BMC Bioinformatics·Gaston K Mazandu, Nicola J Mulder
Jul 10, 2008·Genetic Epidemiology·Janna E HutzMichael A Province
May 31, 2019·Nucleic Acids Research·Joana Carlevaro-FitaJianwei Li

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Software Mentioned

GFSST
DynGO
Gene Functional Similarity Search Tool ( GFSST )
BLAST
TrEMBL
GO Graph
GOToolBox
Gene Sorter
UCSC Gene Sorter
UCSC Browser

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