title: ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs.
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.
  
  
  BACKGROUND
  The database is available for free at http://bioinfo.aau.ac.in/ESMP.
authors.affiliation: Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat- 785013, Assam, India.
authors.forename: Ranjan
authors.initials: R
authors.lastname: Sarmah
authors.forename: Jagajjit
authors.initials: J
authors.lastname: Sahu
authors.forename: Budheswar
authors.initials: B
authors.lastname: Dehury
authors.forename: Kishore
authors.initials: K
authors.lastname: Sarma
authors.forename: Smita
authors.initials: S
authors.lastname: Sahoo
authors.forename: Mousumi
authors.initials: M
authors.lastname: Sahu
authors.forename: Madhumita
authors.initials: M
authors.lastname: Barooah
authors.forename: Priyabrata
authors.initials: P
authors.lastname: Sen
authors.forename: Mahendra Kumar
authors.initials: MK
authors.lastname: Modi