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tacg – a grep for DNA
BACKGROUND: Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interes...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2002
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99049/ https://www.ncbi.nlm.nih.gov/pubmed/11882250 http://dx.doi.org/10.1186/1471-2105-3-8 |
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author | Mangalam, Harry J |
author_facet | Mangalam, Harry J |
author_sort | Mangalam, Harry J |
collection | PubMed |
description | BACKGROUND: Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple motifs with IUPAC degeneracies, regular expressions, patterns allowing mismatches, and probability matrices. RESULTS: I describe a small application which allows searching for all the above pattern types individually, which further allows these atomic motifs to be assembled into logical rules for more sophisticated analysis. CONCLUSION: tacg is small, portable, faster and more capable than most alternatives, relatively easy to modify, and freely available in source code. |
format | Text |
id | pubmed-99049 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2002 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-990492002-03-22 tacg – a grep for DNA Mangalam, Harry J BMC Bioinformatics Methodology article BACKGROUND: Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple motifs with IUPAC degeneracies, regular expressions, patterns allowing mismatches, and probability matrices. RESULTS: I describe a small application which allows searching for all the above pattern types individually, which further allows these atomic motifs to be assembled into logical rules for more sophisticated analysis. CONCLUSION: tacg is small, portable, faster and more capable than most alternatives, relatively easy to modify, and freely available in source code. BioMed Central 2002-03-06 /pmc/articles/PMC99049/ /pubmed/11882250 http://dx.doi.org/10.1186/1471-2105-3-8 Text en Copyright ©2002 Mangalam; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Methodology article Mangalam, Harry J tacg – a grep for DNA |
title | tacg – a grep for DNA |
title_full | tacg – a grep for DNA |
title_fullStr | tacg – a grep for DNA |
title_full_unstemmed | tacg – a grep for DNA |
title_short | tacg – a grep for DNA |
title_sort | tacg – a grep for dna |
topic | Methodology article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99049/ https://www.ncbi.nlm.nih.gov/pubmed/11882250 http://dx.doi.org/10.1186/1471-2105-3-8 |
work_keys_str_mv | AT mangalamharryj tacgagrepfordna |