title: SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.
abstract: Simple Sequence Repeats (SSRs) are used to address a variety of research questions in a variety of fields (e.g. population genetics, phylogenetics, forensics, etc.), due to their high mutability within and between species. Here, we present an innovative algorithm, SA-SSR, based on suffix and longest common prefix arrays for efficiently detecting SSRs in large sets of sequences. Existing SSR detection applications are hampered by one or more limitations (i.e. speed, accuracy, ease-of-use, etc.). Our algorithm addresses these challenges while being the most comprehensive and correct SSR detection software available. SA-SSR is 100% accurate and detected >1000 more SSRs than the second best algorithm, while offering greater control to the user than any existing software.
  
  
  
  SA-SSR is freely available at http://github.com/ridgelab/SA-SSR CONTACT: perry.ridge@byu.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: B D
authors.initials: BD
authors.lastname: Pickett
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: S M
authors.initials: SM
authors.lastname: Karlinsey
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: C E
authors.initials: CE
authors.lastname: Penrod
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: M J
authors.initials: MJ
authors.lastname: Cormier
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: M T W
authors.initials: MT
authors.lastname: Ebbert
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: D K
authors.initials: DK
authors.lastname: Shiozawa
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: C J
authors.initials: CJ
authors.lastname: Whipple
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT 84602, USA.
authors.forename: P G
authors.initials: PG
authors.lastname: Ridge
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D005819:Genetic Markers; D018895:Microsatellite Repeats; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D005819:Genetic Markers