Standalone EST microsatellite mining and analysis tool (SEMAT): for automated EST-SSR analysis in plants

Public databases contain large datasets of plant expressed sequence tags (ESTs) that can be used for mining microsatellite/simple sequence repeat markers. The identification and annotation of these markers take considerable time. Here, we describe an efficient, high-throughput microsatellite mining,...

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Bibliographic Details
Published in:Tree genetics & genomes 2014-12, Vol.10 (6), p.1755-1757
Main Authors: Asari, Naganeeswaran Sudalaimuthu, Ramaswamy, Manimekalai, Subbian, Elain Apshara, Palliyarakkal, Manju Kalathil, Malhotra, S. K, Karun, Anitha
Format: Article
Language:English
Subjects:
Annotations
Automation
Bioinformatics
Biomedical and Life Sciences
Biotechnology
data collection
expressed sequence tags
Forestry
Genomes
Life Sciences
microsatellite repeats
Perl
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Research centers
Short Communication
Software
Tree Biology
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Description
Summary:Public databases contain large datasets of plant expressed sequence tags (ESTs) that can be used for mining microsatellite/simple sequence repeat markers. The identification and annotation of these markers take considerable time. Here, we describe an efficient, high-throughput microsatellite mining, and analysis pipeline, standalone EST microsatellite mining and analysis tool (SEMAT). The pipeline bundles sequence trimming, assembly, microsatellite identification, primer selection, and blast annotation, for which it consecutively uses SeqClean, CAP3, MISA, Primer3, and Blast. SEMAT is written using Perl scripts, and it runs under Ubuntu and Fedora Linux. SEMAT is an efficient and time-saving bioinformatics tool to accomplish the high throughput EST-SSR analysis. It is freely available from http://semat.cpcribioinformatics.in/ .
ISSN:1614-2942
1614-2950
DOI:10.1007/s11295-014-0785-2