Title

Authors

Affiliation

¹Senior Research Fellow, DIT- Agribioinformatics Promotion centre, Central Plantation Crops Research Institute, P. O. Kudlu, Kasaragod-671124, Kerala, India; ²Senior Scientist, Molecular biology and Biotechnology, Crop Improvement Division, Central Plantation Crops Research Institute, P. O. Kudlu, Kasaragod-671124, Kerala, India; ³Principal Scientist, Horticulture Section, ICAR Research Complex for Goa, Old Goa 403 402, India

Email

rmanimekalai@rediffmail.com; *Corresponding author

Article Type

Hypothesis

Date

Received November 16, 2011; Accepted November 16, 2011; Published December 10, 2011

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.

Keywords

Seqclean, SSR, MISA, repeats, Arecacea.

Citation

Palliyarakkal et al. Bioinformation 7(7): 347-351 (2011)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.