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Title

ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs 

Authors

Ranjan Sarmah, Jagajjit Sahu, Budheswar Dehury, Kishore Sarma, Smita Sahoo, Mousumi Sahu, Madhumita Barooah, Priyabrata Sen and Mahendra Kumar Modi*

 

Affiliation

Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, Assam, India

 

Email

mkmodi@gmail.com; *Corresponding author

 

Article Type

Server

Date

Received February 01, 2012; Accepted February 11, 2012; Published February 28, 2012

 

Abstract

With the advent of high-throughput sequencing technology, sequences from many genomes are being deposited to public databases at a brisk rate. Open access to large amount of expressed sequence tag (EST) data in the public databases has provided a powerful platform for simple sequence repeat (SSR) development in species where sequence information is not available. SSRs are markers of choice for their high reproducibility, abundant polymorphism and high inter-specific transferability. The mining of SSRs from ESTs requires different high-throughput computational tools that need to be executed individually which are computationally intensive and time consuming. To reduce the time lag and to streamline the cumbersome process of SSR mining from ESTs, we have developed a user-friendly, web-based EST-SSR pipeline “EST-SSR-MARKER PIPELINE (ESMP)”. This pipeline integrates EST pre-processing, clustering, assembly and subsequently mining of SSRs from assembled EST sequences. The mining of SSRs from ESTs provides valuable information on the abundance of SSRs in ESTs and will facilitate the development of markers for genetic analysis and related applications such as marker-assisted breeding.

 

Availability

http://bioinfo.aau.ac.in/ESMP

 

Keywords

Expressed Sequence Tag, Simple Sequence Repeats, ESMP, Single Nucleotide Polymorphism.

 

Citation

Sarmah et al. Bioinformation 8(4): 206-208(2012)
 

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.