mkESA: enhanced suffix array construction tool

Bioinformatics. 2009 Apr 15;25(8):1084-5. doi: 10.1093/bioinformatics/btp112. Epub 2009 Feb 26.


We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data.

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Sequence Analysis / methods*
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, Protein / methods
  • Sequence Analysis, RNA / methods
  • Software*