find_max_cover

Conant G. C. and Wagner A.

This is the home page for the find_max_cover program. This program will find the combination of local alignments that covers the maximum number of residues in a query sequence.

Citation:

Conant, G. C., and A. Wagner, (2004) A fast algorithm for determining the best combination of local alignments to a query sequence, BMC Bioinformatics, 5: 62. [PDF]

Downloading find_max_cover:

find_max_cover.tar: Source code: An uncompressed tar file contain the source code and a Makefile for GCC/Linux
find_max_cover.exe: Win9X/WinNT/Win2K/WinXP executable version of find_max_cover: compiled with Visual C++ 6.0

Building find_max_cover:

To build under Linux or other platforms with g++, type
% tar xvf find_max_cover.tar
% cd find_max_cover
% make

You make need to modify the makefile for platforms without g++.

find_max_cover Documentation (PDF)

Example program input and output:

Below are three example input files for find_max_cover. The differences between these files is described in the documentation above. The correct output from these inputs is also provided:

Cases when E-values are not desired

Command: find_max_cover example_noeval.txt
Input
Output

Cases when E-values are desired and the overlap parameter is set to 0

Command: find_max_cover example_eval_o0.txt -o:0 -e
Input
Output

Cases when E-values are desired and the overlap is non-zero

Command: find_max_cover example_eval_overlap.txt -o:5 -e
Input
Output
Additional Files required for this analysis:

Cases where alignment scores are used as an optimality criterion

Comand: find_max_cover example_score_calc_overlap.txt -s -o:10
Input
Output
Additional Files

The BLOSUM62 matrix is built into find_max_cover. To use other matrices (such as PAM250), you will need those matrices to follow the format show here.

Contact Information:

Further questions and problems should be reported to Gavin Conant: email: gconant@unm.edu

Disclaimer:

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

To receive a hard copy of the GNU General Public License write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA