mkESA: enhanced suffix array construction tool
AbstractAbstract Summary: 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. Availability: The source code of mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 at http://bibiserv.techfak.uni-bielefeld.de/mkesa/ . Contact: email@example.com © 2009 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.