NAME

GH::Align - a perl package for doing alignments

SYNOPSIS

# this example (and this man page) may be out of date.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.

DESCRIPTION

GH::Align supplies a set of routines for doing sequence alignments.

EXPORT

None by default.

EXPORT_OK

globalMinDifferences boundedGlobalMinDifferences

BUGS

Not so far.

AUTHOR

George Hartzell, hartzell@cs.berkeley.edu

SEE ALSO

GH::Status GH::MspTools

perl(1)