Bio::AlignIO::psi(3)

NAME
Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files

SYNOPSIS
This module will parse PSI-BLAST output of the format seqid XXXX

DESCRIPTION
This is a parser for psi-blast blocks.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
Email jason@bioperl.org

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $obj = Bio::AlignIO::psi->new();
 Function: Builds a new Bio::AlignIO::psi object
 Returns : Bio::AlignIO::psi
 Args    :

  next_aln
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream
 Returns : Bio::Align::AlignI object
 Args    : NONE

See Bio::Align::AlignI

  write_aln
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the NCBI psi-format object (.aln) into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object

Bio::Align::AlignI