---
name: "Bio::AlignIO::psi"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::AlignIO::psi"
---

# Bio::AlignIO::psi(3pm)

Read/Write PSI-BLAST profile alignment files

## 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:

```
  https://github.com/bioperl/bioperl-live/issues
```

## 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