HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data
Autor(es): Churbanov, Alexander; Ryan, Rachael; Hasan, Nabeeh; Bailey, Donovan; Chen, Haofeng; Milligan, Brook; Houde, Peter
Resumo: Microsatellites are among the most useful genetic markers in population biology. High-throughput sequencing of microsatellite-enriched libraries dramatically expedites the traditional process of screening recombinant libraries for microsatellite markers. However, sorting through millions of reads to distill high-quality polymorphic markers requires special algorithms tailored to tolerate sequencing errors in locus reconstruction, distinguish paralogous loci, rarify raw reads originating from the same amplicon and sort out various artificial fragments resulting from recombination or concatenation of auxiliary adapters. Existing programs warrant improvement.Results: We describe a microsatellite prediction framework named for microsatellite genotyping based on high-throughput sequencing. We demonstrate the utility of in comparison to Roche on two Roche 454 GS FLX runs. The majority of the -assembled loci were reliably mapped against model organism reference genomes. demultiplexes pooled libraries, assesses locus polymorphism and implements for the design of PCR primers flanking polymorphic microsatellite loci. As sequencing costs drop and permit the analysis of all project samples on next-generation platforms, this framework can also be used for direct simple Sequence repeats genotyping.
Palavras-Chave: Tandem Repeats; Microsatellite Markers; Genomic Sequences; Simple Algorithm; Primer Design; Alignment; Search; Dna; Program; Muscle
Imprenta: Bioinformatics, v. 28, n. 21, p. 2797-2803, 2012
Identificador do objeto digital: 10.1093/bioinformatics/bts524
Descritores: Aedes aegypti - Molecular screening
Data de publicação: 2012
