Standalone EST microsatellite mining and analysis tool (SEMAT): for automated EST-SSR analysis in plants
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Date
2014
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Abstract
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 timesaving
bioinformatics tool to accomplish the high throughput
EST-SSR analysis. It is freely available from http://semat.
cpcribioinformatics.in/.
Description
Keywords
EST, Microsatellite, Pipeline, Tool
Citation
Tree Genetics & Genomes (2014) 10:1755–1757