Not AvailableMicrosatellites are ubiquitously distributed, polymorphic repeat sequence valuable for
association, selection, population structure and identification. They can be mined by
genomic library, probe hybridization and sequencing of selected clones. Such approach
has many limitations like biased hybridization and selection of larger repeats. In silico
mining of polymorphic markers using data of various genotypes can be rapid and
economical. Available tools lack in some or other aspects like: targeted user defined
primer generation, polymorphism discovery using multiple sequence, size and number
limits of input sequence, no option for primer generation and e-PCR evaluation,
transferability, lack of complete automation and user-friendliness. They also lack the
provision to evaluate published primers in e-PCR mode to generate additional allelic
data using re-sequenced data of various genotypes for judicious utilization of previously
generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and
launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It
mines microsatellite loci and computes primers from genome/transcriptome data of any
species. It can perform e-PCR using published primers for polymorphism discovery and
across species transferability of microsatellite loci. Present tool has been evaluated using
five species of different genome size having 21 genotypes. Though server is equipped
with genomic data of three species for test run with gel simulation, but can be used for
any species. Further, polymorphism predictability has been validated using in silico and
in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite
polymorphism discovery in re-sequencing projects of any species of plant and animal
for their diversity estimation along with variety/breed identification, population structure,
MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and
genome finishing.Not Availabl
