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mkESA - enhanced suffix array construction tool

Introduction

mkESA is an open source program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on our implementation of Manzini's lightweight Deep-Shallow algorithm [1], which can also utilize multiple CPUs/cores for some extra speed-up. The generated output is compatible with the output of mkvtree from the Vmatch package written by Stefan Kurtz.

mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 or higher. Try our download page.

Installation

After extraction, use something like

$ ./configure [options] && make && make install

to configure, build, and install the program. Optionally, run make check before installation to run the test suite. All tests should pass with no error. By default, make install will install the program below /usr/local/. Read the output of ./configure --help to learn more about configuration options.

Please note that mkESA is based on our library libfid, which needs to be built and installed beforehand. If libfid is not installed in a system-wide path, you need to tell the configure script where to find it, like --with-libfid-prefix=path_to_lib. A typical command for configuring mkESA using gcc with threads enabled and libfid installed in a system-wide location looks like this:

$ ./configure --enable-threads CFLAGS='-O3 -fomit-frame-pointer'

You may also want to add -m64 to CFLAGS in order to build a 64 bit binary if your system supports these (only necessary in case your 64 bit system defaults to 32 bit userland, like Solaris or Mac OS X).

Problems

Mac OS X: It has been brought to our attention that multithreading does not work reliably on Macs at the moment. The mkesa program is likely to run very slowly and crash when run with option -t (only available if configured with --enable-threads). It is, however, safe to run mkesa single-threaded, no matter if configured with --enable-threads or not. We are currently working on this issue.

References:

[1] G. Manzini, P. Ferragina. Engineering a Lightweight Suffix Array Construction Algorithm. Algorithmica, 40(1):33-50, 2004.

If you use mkESA in your own research, please cite:

[2] R. Homann, D. Fleer, R. Giegerich, M. Rehmsmeier. mkESA: enhanced suffix array construction tool. Bioinformatics, 25(8):1084-1085, 2009. Download

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Fri Dec 14 12:58:09 2012