mkESA: enhanced suffix array construction tool.
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.
Homann
Robert
R
International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. rhomann@techfak.uni-bielefeld.de
Fleer
David
D
Giegerich
Robert
R
Rehmsmeier
Marc
M
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software