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SSRscanner: a program for reporting distribution and exact location of simple sequence repeats

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are...

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Detalles Bibliográficos
Autores principales: Anwar, Tamanna, Khan, Asad U
Formato: Texto
Lenguaje:English
Publicado: Biomedical Informatics Publishing Group 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891659/
https://www.ncbi.nlm.nih.gov/pubmed/17597863
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author Anwar, Tamanna
Khan, Asad U
author_facet Anwar, Tamanna
Khan, Asad U
author_sort Anwar, Tamanna
collection PubMed
description Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. AVAILABILITY: This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com
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spelling pubmed-18916592007-06-27 SSRscanner: a program for reporting distribution and exact location of simple sequence repeats Anwar, Tamanna Khan, Asad U Bioinformation Software Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. AVAILABILITY: This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com Biomedical Informatics Publishing Group 2006-02-20 /pmc/articles/PMC1891659/ /pubmed/17597863 Text en © 2006 Biomedical Informatics Publishing Group This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Software
Anwar, Tamanna
Khan, Asad U
SSRscanner: a program for reporting distribution and exact location of simple sequence repeats
title SSRscanner: a program for reporting distribution and exact location of simple sequence repeats
title_full SSRscanner: a program for reporting distribution and exact location of simple sequence repeats
title_fullStr SSRscanner: a program for reporting distribution and exact location of simple sequence repeats
title_full_unstemmed SSRscanner: a program for reporting distribution and exact location of simple sequence repeats
title_short SSRscanner: a program for reporting distribution and exact location of simple sequence repeats
title_sort ssrscanner: a program for reporting distribution and exact location of simple sequence repeats
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891659/
https://www.ncbi.nlm.nih.gov/pubmed/17597863
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