GH::Align - a perl package for doing alignments
# this example (and this man page) may be out of date. Think twice. use GH::Align qw(globalMinDifferences boundedGlobalMinDifferences); use GH::Status; # in reality, these would be real sequences. $s1 = "acgcttac"; $s1 = "ttacgcactatcct"; $arrayRef = globalMinDifferences($s1, $s2); $status = $$arrayRef[0]; if ($status != STAT_OK) { # do something drastic } $cost = $$arrayRef[1]; $editOpsRef = $$arrayRef[2]; foreach $op (@{$opsRef}) { print $op->getOpName, " ", $op->getCount; if ($op->getCount == 1) { print " base.\n"; } else { print " bases.\n"; } } $arrayRef = boundedGlobalMinDifferences($s1, $s2, 5); # same as above.
GH::Align supplies a set of routines for doing sequence alignments.
None by default.
globalMinDifferences boundedGlobalMinDifferences
Not so far.
George Hartzell, hartzell@cs.berkeley.edu
GH::Status GH::MspTools
perl(1)
To install GH::Msp, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GH::Msp
CPAN shell
perl -MCPAN -e shell install GH::Msp
For more information on module installation, please visit the detailed CPAN module installation guide.