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

Plant Pathology

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

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.

Original language	English
Pages (from-to)	2097-2098
Number of pages	2
Journal	Bioinformatics
Volume	21
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/bti257
State	Published - May 1 2005

Bibliographical 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.

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.

N1 - 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.

PY - 2005/5/1

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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

Abstract

Bibliographical note

ASJC Scopus subject areas

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