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Bio::SeqIO::gcg - GCG sequence input/output stream


Do not use this module directly. Use it via the Bio::SeqIO class.


This object can transform Bio::Seq objects to and from GCG flat file databases.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.                  - General discussion  - About the mailing lists


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

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 the bugs and their resolution. Bug reports can be submitted via the web:

AUTHORS - Ewan Birney & Lincoln Stein

Email: <> <>


Jason Stajich,


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


 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :


 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: writes the formatted $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : array of Bio::PrimarySeqI object


 Title     : GCG_checksum
 Usage     : $cksum = $gcgio->GCG_checksum($seq);
 Function  : returns a gcg checksum for the sequence specified

             This method can also be called as a class method.
 Example   :
 Returns   : a GCG checksum string
 Argument  : a Bio::PrimarySeqI implementing object


 Title   : _validate_checksum
 Usage   : n/a - internal method
 Function: if parsed gcg sequence contains a checksum field
         : we compare it to a value computed here on the parsed
         : sequence. A checksum mismatch would indicate some
         : type of parsing failure occurred.
 Returns : 1 for success, 0 for failure
 Args    : string containing parsed seq, value of parsed checksum