title: GeneSeer: a sage for gene names and genomic resources.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. olson@cshl.org
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Olson
authors.forename: Tim
authors.initials: T
authors.lastname: Tully
authors.forename: Ravi
authors.initials: R
authors.lastname: Sachidanandam
mesh_terms: D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D030541:Databases, Genetic; D030562:Databases, Protein; D005821:Genetic Techniques; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D009323:Natural Language Processing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D034741:RNA, Small Interfering / Q000378:metabolism; D012984:Software; D009626:Terminology as Topic
chemical_list: D034741:RNA, Small Interfering