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ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs
Ranjan Sarmah1, Jagajjit Sahu, Budheswar Dehury
1Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat- 785013, Assam, India.
Bioinformation
|March 16, 2012
Summary
We developed a user-friendly pipeline (ESMP) to efficiently mine simple sequence repeats (SSRs) from expressed sequence tags (ESTs). This tool streamlines SSR marker development for genetic analysis and marker-assisted breeding.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- High-throughput sequencing generates vast amounts of genomic data.
- Expressed Sequence Tags (ESTs) are valuable for developing genetic markers in under-resourced species.
- Current SSR mining from ESTs is computationally intensive and time-consuming.
Purpose of the Study:
- To develop an efficient, web-based pipeline for mining SSRs from ESTs.
- To streamline the process of SSR marker development.
- To facilitate genetic analysis and marker-assisted breeding.
Main Methods:
- Developed the EST-SSR-MARKER PIPELINE (ESMP), a web-based tool.
- Integrated EST pre-processing, clustering, and assembly.
- Automated the mining of SSRs from assembled EST sequences.
Main Results:
- The ESMP pipeline significantly reduces the time and computational resources required for SSR mining.
- Provides valuable data on SSR abundance in ESTs.
- Facilitates the discovery of novel SSR markers.
Conclusions:
- The ESMP pipeline offers a user-friendly and efficient solution for SSR marker development.
- Accelerates genetic research and breeding applications.
- Enhances the utility of public EST databases.