Bio::DB::SwissProt - Database object interface to SwissProt retrieval use Bio::DB::SwissProt; $sp = new Bio::DB::SwissProt; $seq = $sp->get_Seq_by_id('KPY1_ECOLI'); # SwissProt ID # <4-letter-identifier>_<species 5-letter code> # or ... $seq = $sp->get_Seq_by_acc('P43780'); # SwissProt AC # [OPQ]xxxxx # In fact in this implementation # these methods call the same webscript so you can use # then interchangeably # choose a different server to query $sp = new Bio::DB::SwissProt('-servertype' => 'expasy', '-hostlocation' => 'us'); $seq = $sp->get_Seq_by_id('BOLA_HAEIN'); # SwissProtID SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. This is in contrast to EMBL/GenBank/DDBJ which are archives of protein information. Additional tools for parsing and manipulating swissprot files can be found at ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/. Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the SwissProt database via an expasy retrieval. Perhaps through SRS later. In order to make changes transparent we have host type (currently only expasy) and location (default to switzerland) separated out. This allows the user to pick the closest expasy mirror for running their queries.

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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email Jason Stajich <jason@bioperl.org < Thanks go to Alexandre Gattiker <gattiker@isb-sib.ch> of Swiss Institute of Bioinformatics for helping point us in the direction of the correct expasy scripts and for swissknife references. Also thanks to Heikki Lehvaslaiho <heikki@ebi.ac.uk> for help with adding EBI swall server. The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Routines from Bio::DB::RandomAccessI

get_Seq_by_id
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception

get_Seq_by_acc
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception

get_Stream_by_id
Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries

get_Stream_by_acc
Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id()

get_Stream_by_batch
Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from SwissProt 'en masse', rather than one at a time. This is implemented the same way as get_Stream_by_id, but is provided here in keeping with access methods of NCBI modules. Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers.

Implemented Routines from Bio::DB::WebDBSeqI interface

get_request
Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)

postprocess_data
Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data

default_format
Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none

Bio::DB::SwissProt specific routines

servertype
Title : servertype Usage : my $servertype = $self->servertype $self->servertype($servertype); Function: Get/Set server type Returns : string Args : server type string [optional]

hostlocation
Title : hostlocation Usage : my $location = $self->hostlocation() $self->hostlocation($location) Function: Set/Get Hostlocation Returns : string representing hostlocation Args : string specifying hostlocation [optional]

location_url
Title : location Usage : my $url = $self->location_url() Function: Get host url Returns : string representing url Args : none

request_format
Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format