TruMatch - A BLAST post-processor that identifies bona fide sequence matches to genome assemblies

Weixi Li; Cathryn J. Rehmeyer; Chuck Staben; Mark L. Farman

doi:10.1093/bioinformatics/bti257

TruMatch - A BLAST post-processor that identifies bona fide sequence matches to genome assemblies

Weixi Li
, Cathryn J. Rehmeyer
, Chuck Staben
, Mark L. Farman

Producción científica: Article › revisión exhaustiva

6 Citas (Scopus)

Resumen

Summary: BLAST is a widely used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs, HSPs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may be easily overlooked. To rectify this problem, we developed TruMatch - a program that parses standard BLAST outputs and identifies HSPs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output.

Idioma original	English
Páginas (desde-hasta)	2097-2098
Número de páginas	2
Publicación	Bioinformatics
Volumen	21
N.º	9
DOI	https://doi.org/10.1093/bioinformatics/bti257
Estado	Published - may 1 2005

Nota bibliográfica

Funding Information:
Thanks to Chris Schardl for his critical review of the manuscript. This work was supported by a subcontract to Chuck Staben from the Kentucky Biomedical Research Infrastructure Network, 5P20RR016481-03, awarded to Nigel Cooper of the University of Louisville, by the National Center for Research Resources and by a National Science Foundation award, MCB-0135462, to Mark Farman. This is Kentucky Agricultural Experiment Station publication #05-12-004.

Financiación

Thanks to Chris Schardl for his critical review of the manuscript. This work was supported by a subcontract to Chuck Staben from the Kentucky Biomedical Research Infrastructure Network, 5P20RR016481-03, awarded to Nigel Cooper of the University of Louisville, by the National Center for Research Resources and by a National Science Foundation award, MCB-0135462, to Mark Farman. This is Kentucky Agricultural Experiment Station publication #05-12-004.

Financiadores	Número del financiador
Kentucky Biomedical Research Infrastructure Network Bioinformatics Core	5P20RR016481-03
National Science Foundation (NSF)	MCB-0135462
National Center for Research Resources
University of Louisville

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bti257

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title = "TruMatch - A BLAST post-processor that identifies bona fide sequence matches to genome assemblies",

abstract = "Summary: BLAST is a widely used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs, HSPs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may be easily overlooked. To rectify this problem, we developed TruMatch - a program that parses standard BLAST outputs and identifies HSPs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output.",

author = "Weixi Li and Rehmeyer, \{Cathryn J.\} and Chuck Staben and Farman, \{Mark L.\}",

note = "Funding Information: Thanks to Chris Schardl for his critical review of the manuscript. This work was supported by a subcontract to Chuck Staben from the Kentucky Biomedical Research Infrastructure Network, 5P20RR016481-03, awarded to Nigel Cooper of the University of Louisville, by the National Center for Research Resources and by a National Science Foundation award, MCB-0135462, to Mark Farman. This is Kentucky Agricultural Experiment Station publication \#05-12-004.",

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AU - Staben, Chuck

AU - Farman, Mark L.

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N2 - Summary: BLAST is a widely used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs, HSPs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may be easily overlooked. To rectify this problem, we developed TruMatch - a program that parses standard BLAST outputs and identifies HSPs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output.

AB - Summary: BLAST is a widely used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs, HSPs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may be easily overlooked. To rectify this problem, we developed TruMatch - a program that parses standard BLAST outputs and identifies HSPs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output.

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TruMatch - A BLAST post-processor that identifies bona fide sequence matches to genome assemblies

Resumen

Nota bibliográfica

Financiación

ASJC Scopus subject areas

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Huella

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