JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences

We describe the use of Java Pattern Finder (JaPaFi) to identify short (<100 nt) highly conserved sequences in a series of poxvirus genomes. The algorithm utilizes pattern matching to identify approximate matches appearing at least once in each member of a set of genomes; a key feature is that the...

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Detalles Bibliográficos
Autores principales: Sadeque, Aliya, Barsky, Marina, Marass, Francesco, Kruczkiewicz, Peter, Upton, Chris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2010
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185747/
https://www.ncbi.nlm.nih.gov/pubmed/21994712
http://dx.doi.org/10.3390/v2091867
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author Sadeque, Aliya
Barsky, Marina
Marass, Francesco
Kruczkiewicz, Peter
Upton, Chris
author_facet Sadeque, Aliya
Barsky, Marina
Marass, Francesco
Kruczkiewicz, Peter
Upton, Chris
author_sort Sadeque, Aliya
collection PubMed
description We describe the use of Java Pattern Finder (JaPaFi) to identify short (<100 nt) highly conserved sequences in a series of poxvirus genomes. The algorithm utilizes pattern matching to identify approximate matches appearing at least once in each member of a set of genomes; a key feature is that the genomes do not need to be aligned. The user simply specifies the genomes to search, minimum length of sequences to find and the maximum number of mismatches and indels allowed. Many of the most highly conserved segments contain poxvirus promoter elements.
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spelling pubmed-31857472011-10-12 JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences Sadeque, Aliya Barsky, Marina Marass, Francesco Kruczkiewicz, Peter Upton, Chris Viruses Article We describe the use of Java Pattern Finder (JaPaFi) to identify short (<100 nt) highly conserved sequences in a series of poxvirus genomes. The algorithm utilizes pattern matching to identify approximate matches appearing at least once in each member of a set of genomes; a key feature is that the genomes do not need to be aligned. The user simply specifies the genomes to search, minimum length of sequences to find and the maximum number of mismatches and indels allowed. Many of the most highly conserved segments contain poxvirus promoter elements. Molecular Diversity Preservation International (MDPI) 2010-08-31 /pmc/articles/PMC3185747/ /pubmed/21994712 http://dx.doi.org/10.3390/v2091867 Text en © 2010 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Sadeque, Aliya
Barsky, Marina
Marass, Francesco
Kruczkiewicz, Peter
Upton, Chris
JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
title JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
title_full JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
title_fullStr JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
title_full_unstemmed JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
title_short JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
title_sort japafi: a novel program for the identification of highly conserved dna sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185747/
https://www.ncbi.nlm.nih.gov/pubmed/21994712
http://dx.doi.org/10.3390/v2091867
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