SA-SSR

SA-SSR is a tool to locate Simple Sequence Repeats (SSRs) in DNA or RNA sequences. The SA-SSR algorithm uses suffix and longest common prefix arrays in the detection.

Topic

Sequencing;DNA;RNA;Sequence sites, features and motifs

Detail

  • Operation: Nucleic acid feature detection

  • Software interface: Command-line user interface

  • Language: C++

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: This work was supported by start-up funds from Brigham Young University to PGR and a mentoring environment grant from Brigham Young University to CJW.

  • Input: FASTA

  • Output: -

  • Contact: Pery G Ridge perry.ridge@byu.edu

  • Collection: -

  • Maturity: -

Publications

  • SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.
  • Pickett BD, Karlinsey SM, Penrod CE, Cormier MJ, Ebbert MT, Shiozawa DK, Whipple CJ, Ridge PG. SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences. Bioinformatics. 2016 Sep 1;32(17):2707-9. doi: 10.1093/bioinformatics/btw298. Epub 2016 May 11. PMID: 27170037; PMCID: PMC5013907.
  • https://doi.org/10.1093/bioinformatics/btw298
  • PMID: 27170037
  • PMC: PMC5013907

Download and documentation

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