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Microsatellites in palm (Arecaceae) sequences

Microsatellites are the most promising co-dominant markers, widely distributed throughout the genome. Identification of these repeating genomic subsets is a tedious and iterative process making computational approaches highly useful for solving this biological problem. Here 38,083 microsatellites we...

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Autores principales: Palliyarakkal, Manju Kalathil, Ramaswamy, Manimekalai, Vadivel, Arunachalam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280489/
https://www.ncbi.nlm.nih.gov/pubmed/22355235
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author Palliyarakkal, Manju Kalathil
Ramaswamy, Manimekalai
Vadivel, Arunachalam
author_facet Palliyarakkal, Manju Kalathil
Ramaswamy, Manimekalai
Vadivel, Arunachalam
author_sort Palliyarakkal, Manju Kalathil
collection PubMed
description Microsatellites are the most promising co-dominant markers, widely distributed throughout the genome. Identification of these repeating genomic subsets is a tedious and iterative process making computational approaches highly useful for solving this biological problem. Here 38,083 microsatellites were localized in palm sequences. A total of 2, 97,023 sequences retrieved from public domains were used for this study. The sequences were unstained using the tool Seqclean and consequently clustered using CAP3. SSRs are located in the sequences using the microsatellite search tool, MISA. Repeats were detected in 33,309 sequences and more than one SSR had appeared in 3,943 sequences. In the present study, dinucleotide repeats (49%) were found to be more abundant followed by mononucleotide (30%) and trinucleotide (19%). Also among the dinucleotides, AG/GA/TC/CT motifs (55.8%) are predominantly repeating within the palm sequences. Thus in future this study will lead to the development of specific algorithm for mining SSRs exclusively for palms.
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spelling pubmed-32804892012-02-21 Microsatellites in palm (Arecaceae) sequences Palliyarakkal, Manju Kalathil Ramaswamy, Manimekalai Vadivel, Arunachalam Bioinformation Hypothesis Microsatellites are the most promising co-dominant markers, widely distributed throughout the genome. Identification of these repeating genomic subsets is a tedious and iterative process making computational approaches highly useful for solving this biological problem. Here 38,083 microsatellites were localized in palm sequences. A total of 2, 97,023 sequences retrieved from public domains were used for this study. The sequences were unstained using the tool Seqclean and consequently clustered using CAP3. SSRs are located in the sequences using the microsatellite search tool, MISA. Repeats were detected in 33,309 sequences and more than one SSR had appeared in 3,943 sequences. In the present study, dinucleotide repeats (49%) were found to be more abundant followed by mononucleotide (30%) and trinucleotide (19%). Also among the dinucleotides, AG/GA/TC/CT motifs (55.8%) are predominantly repeating within the palm sequences. Thus in future this study will lead to the development of specific algorithm for mining SSRs exclusively for palms. Biomedical Informatics 2011-12-10 /pmc/articles/PMC3280489/ /pubmed/22355235 Text en © 2011 Biomedical Informatics 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 Hypothesis
Palliyarakkal, Manju Kalathil
Ramaswamy, Manimekalai
Vadivel, Arunachalam
Microsatellites in palm (Arecaceae) sequences
title Microsatellites in palm (Arecaceae) sequences
title_full Microsatellites in palm (Arecaceae) sequences
title_fullStr Microsatellites in palm (Arecaceae) sequences
title_full_unstemmed Microsatellites in palm (Arecaceae) sequences
title_short Microsatellites in palm (Arecaceae) sequences
title_sort microsatellites in palm (arecaceae) sequences
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280489/
https://www.ncbi.nlm.nih.gov/pubmed/22355235
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