Benjamin Booth

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  # this example (and this man page) may be out of date.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