Microsatellites in palm (Arecaceae) sequences.

Bioinformation
Manju Kalathil PalliyarakkalArunachalam Vadivel

Abstract

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.

Citations

Mar 22, 2014·Molecular Genetics and Genomics : MGG·Ali Akbar Asadi, Sajad Rashidi Monfared
Jul 9, 2016·BMC Research Notes·Karim SorkhehPedro Martínez-Gómez

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Software Mentioned

Seqclean
Excel
CAP3
MISA
MISA perl script
UniVec
MIcroSAtellite ( MISA )

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