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.
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.
Source code: An uncompressed tar file contain the source code and a Makefile
Win9X/WinNT/Win2K/WinXP executable version of find_max_cover: compiled
with Visual C++ 6.0
To build under Linux or other platforms with g++, type
% tar xvf find_max_cover.tar
% cd find_max_cover
You make need to modify the makefile for platforms without g++.
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:
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
Cases when E-values are not desired
Command: find_max_cover example_noeval.txt
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
Cases when E-values are desired and the overlap is non-zero
Command: find_max_cover example_eval_overlap.txt -o:5 -e
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
Further questions and problems should be reported to Gavin Conant: email:
Copyright © 2003 Gavin Conant and Andreas Wagner
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
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,