GeneSeer: a sage for gene names and genomic resources

Olson, A. J., Tully, T., Sachidanandam, R. (2005) GeneSeer: a sage for gene names and genomic resources. BMC Genomics, 6 (1). p. 134. ISSN 1471-2164 (Electronic)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/16176584
DOI: 10.1186/1471-2164-6-134

Abstract

BACKGROUND: Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homologs in other species and relevant publications. METHODS: We solve the naming problem by collecting data from a variety of sources and building a name-translation database. We have also built a table of homologs across several model organisms: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae, S. pombe and A. thaliana. This allows GeneSeer to draw phylogenetic trees and identify the closest homologs. This, in turn, allows the use of names from one species to identify homologous genes in another species. A website http://geneseer.cshl.org/ is connected to the database to allow user-friendly access to our tools and external genomic resources using familiar gene names. CONCLUSION: GeneSeer allows access to gene information through common names and can map sequences to names. GeneSeer also allows identification of homologs and paralogs for a given gene. A variety of genomic data such as sequences, SNPs, splice variants, expression patterns and others can be accessed through the GeneSeer interface. It is freely available over the web http://geneseer.cshl.org/ and can be incorporated in other tools through an http-based software interface described on the website. It is currently used as the search engine in the RNAi codex resource, which is a portal for short hairpin RNA (shRNA) gene-silencing constructs.

Item Type: Paper
Uncontrolled Keywords: Alternative Splicing Computational Biology methods Database Management Systems Databases, Factual Databases Genetic Databases Protein Genetic Techniques Genome Genomics methods Humans Information Storage and Retrieval Internet Natural Language Processing Phylogeny Polymorphism Single Nucleotide RNA Small Interfering metabolism Software Terminology
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > databases > databases
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > genes: types
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > siRNA
CSHL Authors:
Communities: CSHL labs > Sachidanandam lab
Depositing User: CSHL Librarian
Date: 2005
Date Deposited: 06 Jan 2012 20:17
Last Modified: 03 Nov 2017 16:01
PMCID: PMC1266031
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22668

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