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Microsatellites in palm (Arecaceae) sequences

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Author(s): Manju Kalathil Palliyarakkal | Manimekalai Ramaswamy | Arunachalam Vadivel

Journal: Bioinformation
ISSN 0973-2063

Volume: 7;
Issue: 7;
Start page: 347;
Date: 2011;
Original page

Keywords: Seqclean | SSR | MISA | repeats | Arecacea

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.
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