pfam

By aggregator | September 22, 2011

This service allows you to access and retrieve data from the pfam database. The Pfam database is a large collection of protein domain families. Each family is represented by multiple sequence alignments and hidden Markov models (HMMs).

To return the accession and ID for a Pfam family, given either the ID or accession as input. Any of the following URLs will return the same simple XML document:

http://pfam.sanger.ac.uk/family/acc?id=Piwi&output=xml

http://pfam.sanger.ac.uk/family/acc/Piwi?output=xml

http://pfam.sanger.ac.uk/family/id?output=xml&acc=PF02171

http://pfam.sanger.ac.uk/family/id/Piwi?output=xml

http://pfam.sanger.ac.uk/family?entry=Piwi&output=xml

You can retrieve a sub-set of the data in a Pfam-A family page as an XML document using any of the following styles of URL:

http://pfam.sanger.ac.uk/family?id=Piwi&output=xml

http://pfam.sanger.ac.uk/family?output=xml&acc=PF02171

http://pfam.sanger.ac.uk/family?entry=Piwi&output=xml

http://pfam.sanger.ac.uk/family/Piwi?output=xml

The last two styles, using the entry parameter or an extended URL, accept either accessions or identifiers. The accession/ID is case-insensitive in all cases.

You can retrieve a list of all Pfam-A families in the latest Pfam release, either as an XML document or as a tab-delimited text file. Both formats contain the Pfam-A accession, Pfam-A identifier and description:

http://pfam.sanger.ac.uk/families?output=xml

http://pfam.sanger.ac.uk/families?output=text

You can also view the list in a web browser by removing the output=xml parameter from the URL.

You can retrieve a sub-set of the data in a protein page as an XML document using any of the following styles of URL:

http://pfam.sanger.ac.uk/protein?id=CANX_CHICK&output=xml

http://pfam.sanger.ac.uk/protein?output=xml&acc=P00789

http://pfam.sanger.ac.uk/protein?entry=P00789&output=xml

http://pfam.sanger.ac.uk/protein/P00789?output=xml

As for Pfam-A families, arguments are all case-insensitive and the entry parameter accepts either ID or accession.

Name

pfam

Documentation

http://pfam.sanger.ac.uk/help

Protocol

REST

WSDL

Endpoint

http://pfam.sanger.ac.uk/

Topic

Biology, Domains, Motifs, Repeats

Type

Analysis, Data Retrieval, Identifier

Tags

motifs, protein domain, protein family, Protein Motifs, Proteomics

Description

This service allows you to access and retrieve data from the pfam database. The Pfam database is a large collection [...]

Further information

To return the accession and ID for a Pfam family, given either the ID or accession as input. Any of the following URLs will return the same simple XML document:

http://pfam.sanger.ac.uk/family/acc?id=Piwi&output=xml

http://pfam.sanger.ac.uk/family/acc/Piwi?output=xml

http://pfam.sanger.ac.uk/family/id?output=xml&acc=PF02171

http://pfam.sanger.ac.uk/family/id/Piwi?output=xml

http://pfam.sanger.ac.uk/family?entry=Piwi&output=xml

You can retrieve a sub-set of the data in a Pfam-A family page as an XML document using any of the following styles of URL:

http://pfam.sanger.ac.uk/family?id=Piwi&output=xml

http://pfam.sanger.ac.uk/family?output=xml&acc=PF02171

http://pfam.sanger.ac.uk/family?entry=Piwi&output=xml

http://pfam.sanger.ac.uk/family/Piwi?output=xml

The last two styles, using the entry parameter or an extended URL, accept either accessions or identifiers. The accession/ID is case-insensitive in all cases.

http://pfam.sanger.ac.uk/families?output=xml

http://pfam.sanger.ac.uk/families?output=text

You can also view the list in a web browser by removing the output=xml parameter from the URL.

You can retrieve a sub-set of the data in a protein page as an XML document using any of the following styles of URL:

http://pfam.sanger.ac.uk/protein?id=CANX_CHICK&output=xml

http://pfam.sanger.ac.uk/protein?output=xml&acc=P00789

http://pfam.sanger.ac.uk/protein?entry=P00789&output=xml

http://pfam.sanger.ac.uk/protein/P00789?output=xml

As for Pfam-A families, arguments are all case-insensitive and the entry parameter accepts either ID or accession.

Original source