pfam

By | 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
, , , ,
Description

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

Further information

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.

Original source
BioCatalogue

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