DNA-BAR: Distinguisher selection for DNA barcoding

B. DasGupta; K. M. Konwar; Ion I. Mǎndoiu; A. A. Shvartsman

doi:10.1093/bioinformatics/bti547

DNA-BAR: Distinguisher selection for DNA barcoding

B. DasGupta
, K. M. Konwar
, Ion I. Mǎndoiu
, A. A. Shvartsman

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

47 Scopus citations

Abstract

Summary: DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.

Original language	English (US)
Pages (from-to)	3424-3426
Number of pages	3
Journal	Bioinformatics
Volume	21
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/bti547
State	Published - Aug 15 2005
Externally published	Yes

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/bti547

Cite this

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title = "DNA-BAR: Distinguisher selection for DNA barcoding",

abstract = "Summary: DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.",

author = "B. DasGupta and Konwar, \{K. M.\} and Mǎndoiu, \{Ion I.\} and Shvartsman, \{A. A.\}",

note = "Funding Information: B.D.G. was supported in part by NSF grants CCR-0206795, CCR-0208749 and NSF CAREER grant IIS-0346973. K.M.K. and A.A.S. were supported in part by NSF ITR grant 0121277. I.I.M. was Funding Information: supported in part by a large grant from the University of Connecticut{\textquoteright}s Research Foundation.",

year = "2005",

month = aug,

day = "15",

doi = "10.1093/bioinformatics/bti547",

language = "English (US)",

volume = "21",

pages = "3424--3426",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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}

TY - JOUR

T1 - DNA-BAR

T2 - Distinguisher selection for DNA barcoding

AU - DasGupta, B.

AU - Konwar, K. M.

AU - Mǎndoiu, Ion I.

AU - Shvartsman, A. A.

N1 - Funding Information: B.D.G. was supported in part by NSF grants CCR-0206795, CCR-0208749 and NSF CAREER grant IIS-0346973. K.M.K. and A.A.S. were supported in part by NSF ITR grant 0121277. I.I.M. was Funding Information: supported in part by a large grant from the University of Connecticut’s Research Foundation.

PY - 2005/8/15

Y1 - 2005/8/15

N2 - Summary: DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.

AB - Summary: DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.

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JO - Bioinformatics

JF - Bioinformatics

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DNA-BAR: Distinguisher selection for DNA barcoding

Abstract

ASJC Scopus subject areas

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