Homology search for genes.

Homology search for genes. Research Abstract Details 

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Homology search for genes. Abstract Text:

Xuefeng Cui, Vinar,Brona ,Dennis Shasha,Ming Li,

MOTIVATION: Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs). These HSPs then need to be correlated with existing sequence annotations, or assembled manually into putative gene structures. This process is error-prone and labor-intensive, especially in genomes without reliable gene annotation. RESULTS: We have developed a homology search solution that automates this process, and instead of HSPs returns complete gene structures. We achieve better sensitivity and specificity by adapting a hidden Markov model for gene finding to reflect features of the query gene. Compared to traditional homology search, our novel approach identifies splice sites much more reliably and can even locate exons that were lost in the query gene. On a testing set of 400 mouse query genes, we report 79% exon sensitivity and 80% exon specificity in the human genome based on orthologous genes annotated in NCBI HomoloGene. In the same set, we also found 50 (12%) gene structures with better protein alignment scores than the ones identified in HomoloGene. AVAILABILITY: The Java implementation is available for download from http://www.bioinformatics.uwaterloo.ca/software.

Homology search for genes. Publishing Authors By Initials

X Cui,T Vinar,B ,D Shasha,M Li,

For similar biochemical phenomena, metabolism, and nutrition: biochemical phenomena: sequence homology: sequence homology, nucleic acid research abstracts see: biochemical phenomena, metabolism, and nutrition: biochemical phenomena: sequence homology: sequence homology, nucleic acid research

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Homology search for genes. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: i97-103

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 1

MONTH: Jul

YEAR: 2007

Homology search for genes. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9808944

Homology search for genes. Keywords Mesh Terms:

KEYWORDS: Sequence Homology, Nucleic Acid

MESH TERMS: methods

Chemical & Substance for Abstract: Homology search for genes. Information

Substance Name: Proteome

Registry Number: 0

Grant and Affiliation Information for Homology search for genes.

AFFILIATION: Cheriton School of Computer Science, University of Waterloo, Ontario, Canada N2L 3G1.

Country: England

AGENCY: United States PHS

GRANT: 22XS013A

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MEDLINETA: Bioinformatics

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