PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data Article Swipe
Ritwika Das
,
Vasu Arora
,
Sarika Jaiswal
,
Mir Asif Iquebal
,
UB Angadi
,
Samar Fatma
,
Rakesh Singh
,
Sandip Shil
,
Anil Rai
,
Dinesh Kumar
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.3389/fpls.2018.01966
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.3389/fpls.2018.01966
Microsatellites 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.
Related Topics
Concepts
Microsatellite
Transcriptome
Biology
Genome
Computational biology
Genetics
Gene
Allele
Gene expression
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fpls.2018.01966
- OA Status
- gold
- Cited By
- 20
- References
- 46
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2909584420
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2909584420Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3389/fpls.2018.01966Digital Object Identifier
- Title
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PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome DataWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2019Year of publication
- Publication date
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2019-01-11Full publication date if available
- Authors
-
Ritwika Das, Vasu Arora, Sarika Jaiswal, Mir Asif Iquebal, UB Angadi, Samar Fatma, Rakesh Singh, Sandip Shil, Anil Rai, Dinesh KumarList of authors in order
- Landing page
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https://doi.org/10.3389/fpls.2018.01966Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.3389/fpls.2018.01966Direct OA link when available
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Microsatellite, Transcriptome, Biology, Genome, Computational biology, Genetics, Gene, Allele, Gene expressionTop concepts (fields/topics) attached by OpenAlex
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20Total citation count in OpenAlex
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2025: 2, 2024: 3, 2023: 5, 2022: 5, 2021: 3Per-year citation counts (last 5 years)
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46Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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