Journal ArticleDOI
msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design
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TLDR
msatcommander is a platform‐independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine, using single‐sequence or concatenated, fasta‐formatted files.Abstract:
msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, fasta-formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8. msatcommander is available from http://code.google.com/p/msatcommander/.read more
Citations
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Journal ArticleDOI
Primer3—new capabilities and interfaces
Andreas Untergasser,Ioana Cutcutache,Triinu Koressaar,Jian Ye,Brant C. Faircloth,Maido Remm,Steven G. Rozen +6 more
TL;DR: Primer3’s current capabilities are described, including more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers.
Journal ArticleDOI
Applications of next generation sequencing in molecular ecology of non-model organisms
Robert Ekblom,Juan Galindo +1 more
TL;DR: A snapshot of the current state of the art for this rapidly advancing and expanding field of research is provided and some likely directions for future developments are given.
Journal ArticleDOI
Current trends in microsatellite genotyping.
Erwan Guichoux,Lélia Lagache,Stefanie Wagner,Stefanie Wagner,Philippe Chaumeil,Patrick Léger,Olivier Lepais,Olivier Lepais,Camille Lepoittevin,Thibaut Malausa,E. Revardel,Franck Salin,Rémy J. Petit +12 more
TL;DR: To make the most of the latest technical developments, the need for a well‐established strategy including standardized high‐throughput bench protocols and specific bioinformatic tools, from primer design to allele calling is outlined.
Journal ArticleDOI
Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing
TL;DR: This study uses high-throughput genomic sequencing technology to produce millions of base pairs of short fragment reads, which were screened with bioinformatics toolsets to identify primers that amplify polymorphic microsatellite loci.
Journal ArticleDOI
Rise of the machines--recommendations for ecologists when using next generation sequencing for microsatellite development.
TL;DR: There are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilized as markers and it is highlighted that the heterogeneity within each group is very large.
References
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Book ChapterDOI
Primer3 on the WWW for general users and for biologist programmers.
Steve Rozen,Helen Skaletsky +1 more
TL;DR: This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs.
Book ChapterDOI
Isolating microsatellite DNA loci
Travis C. Glenn,Nancy A. Schable +1 more
TL;DR: A series of techniques are presented to construct genomic DNA libraries highly enriched for microsatellite DNA loci, making it possible to reduce the time to identify candidate loci for primer development from most eukaryotic species to as little as 1 week.
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