IDSSR: An Efficient Pipeline for Identifying Polymorphic Microsatellites from a Single Genome Sequence.

ABSTRACT: Simple sequence repeats (SSRs) are known as microsatellites, and consist of tandem 1-6-base motifs. They have become one of the most popular molecular markers, and are widely used in molecular ecology, conservation biology, molecular breeding, and many other fields. Previously reported methods identify monomorphic and polymorphic SSRs and determine the polymorphic SSRs via experimental validation, which is potentially time-consuming and costly. Herein, we present a new strategy named insertion/deletion (INDEL) SSR (IDSSR) to identify polymorphic SSRs by integrating SSRs with nucleotide insertions/deletions (INDEL) solely based on a single genome sequence and the sequenced pair-end reads. These INDEL indexes and polymorphic SSRs were identified, as well as the number of repeats, repeat moti

SUBMITTER: Guang XM 

PROVIDER: S-EPMC6678329 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature