Pfam 22.0 :: Help page: Links Making stable links to Pfam

Making stable links to Pfam/Janelia Farm

Pfam is maintained by a consortium of researchers based in Cambridge, Stockholm, and Janelia Farm. the data files are identical, the web servers are not mirrors of each other; they are maintained separately and only loosely coordinated by code-sharing.

All the servers are in a continuous state of flux, especially near the time of new Pfam releases. Webmasters are not advised to make links to just any Pfam page. However, we promise to make every effort to maintain the following links that other webmasters may find useful. This file only documents the guaranteed URLs for the Janelia Farm Pfam server.

Home page:

http://pfam.janelia.org/

Search server (query submission form)

http://pfam.janelia.org/hmmsearch.shtml

Retrieving Pfam family description pages

Example: retrieve PF0002
http://pfam.janelia.org/cgi-bin/getdesc?acc=PF00002
The Janelia Farm server also supports fetching this page by name; substitute "name=pkinase" (for instance), instead of "acc=PF00002". However, accession numbers are more stable from release to release than names are, so we recommend that you link by accession number.

Retrieving Pfam alignments

Example: retrieve Seed alignment for PF00002:
http://pfam.janelia.org/cgi-bin/getalignment?acc=PF00002&type=seed
Again, substitute "name=pkinase" (for instance) instead of "acc=PFxxxxx" to retrive by name instead of accession. The "type=" variable must be given; it must be either "seed" (for retrieving a Seed alignment) or "full" (for retrieving a Full alignment).

Direct submission to the Pfam search server

Example: submit the peptide "MFTLEV" to a search: http://pfam.janelia.org/cgi-bin/nph-hmmsearch?protseq=MFTLEV&search_mode=merge&cutoff_strategy=ga
All of these variables must be set:

• protseq - Note that you don't put quotes around the sequence.
• search_mode - merge, both, ls, or fs
• cutoff_strategy - ga or evalue, if evalue, then you must also set an 'evalue' variable.

For more information on search options, see the search help pages.

questions or comments:
Howard Hughes Medical Institute