Bayesaligner FAQ

Question: Why can't I compile the Bayes Block Aligner on my platform (linux,SGI...)?
Answer: The only supported platform for the bayes aligner with a GUI front-end is Solaris sparc. The non-GUI version is supported on Microsoft Windows. You can create a non-GUI for linux (and some of the other unix platforms) by doing the following: Copy the source/ directory to your linux machine and then run the makeit.bat file (do "chmod +x makeit.bat" so you that it will run). The gnuplot tools that you use for windows95 will work on linux if have a linux version of gnuplot. To make a GUI version of the bayes aligner takes more work since you have to have the lesstif libraries installed on the linker path and you have to modify the source code for the include files and the makefile to compensate for the differences between solaris and linux.


Question: Why does the Bayes Block Aligner take up so much memory ?
Answer: The bayes aligner is a N*M*K space and time algorithm where:
N=query sequence length
M=data sequence length
k=number blocks
Here is a perl code snip to estimate the space needed for this version.
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if (($ARGV[0] eq "" || ($ARGV[1] eq ""))) {
die "usage: space query_length data_length \n";
}
$space=$ARGV[0]*$ARGV[1]*64.0+$ARGV[0]*24.0;
print "space for alignment = $space bytes or ",$space/1000000," megabytes"," \n";
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to align two sequences of 5000 each will take about 1.6 gigabytes of memory (not to mention several hours of run time)
5000 is as large as you can go since the number of possible alignments overflows a double precision number.


Last modified: Fri Nov 29 11:24:57 EST 2002