Correlated Pattern Discovery program

A program that solves the generalized color set size problem in linear time. (... well, almost. The suffix array implementation currently just uses qsort(). It shouldn't be so slow in practice...)

source code (rev 136) (Nov. 23, 2004)
precompiled binary for x86 Linux (rev 136) (Nov. 23, 2004)
Copyright (C) 2004 Hideo Bannai
(Note: this is a preliminary version with minimal functionality, and may or may not work)

The source code is released under the GNU General Public License. It has been developed and tested mainly on a PC running Linux, and requires the Boost C++ Libraries to compile. There is currently no configure script, so you will need to modify the Makefiles manually if you have any problems compiling the source codes. (There is no install step either)

The program implements the algorithms in the papers:

• Hideo Bannai, Heikki Hyyrö , Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, and Satoru Miyano, "Finding Optimal Pairs of Patterns", In Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI 2004), LNBI 3240:450-462, (2004). (PDF)
• Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, and Satoru Miyano, "Efficiently Finding Regulatory Elements using Correlation with Gene Expression", Journal of Bioinformatics and Computational Biology, 2(2):273-288, (2004). (PDF)

If you have any questions or comments, please contact Hideo Bannai ().