IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Icarus script for stockholm format Pfam anyone ?

Peter Rice pmr at sanger.ac.uk
Fri Oct 8 04:04:21 EST 1999

Thon de Boer <tdeboer at hgmp.mrc.ac.uk> writes:

> Has anyone made a new icarus .is script for the new stockholm format
> of the Pfam database by any chance ?
> The convert script that strips out the stockholm format chokes on the
> new 4.3 release and I can't seems to find an icarus script on the
> sanger-home-of-Pfam-center either.
> If they don't support the new stockholm format....who does ! ;-)

I assume Stockholm format is the horrible mixture of hashes and equals
signs that appeared in Pfam recently.

Yes, we do have a parser. I get to write them first because we index
"PFAMNEW" "PFAMANEW" and so on when a new release is in preparation.
Getting SRS to accept the # character is especially tricky it seems.

SRS5 is very fussy about the Icarus file names, and they have to match
the database names for SRSWWW to serve them up. The .is files seem to
be available for PFAMA etc., but you can't see the .i file (which is
really called pfam.i and defines all the databases) unless you go
through database PFAM.

So, you should find the parser for PFAM which we use on PFAM, PFAMA,
PFAMB and so on. The URL for it is:


I have been thinking about setting up a repository for SRS parsers at
Sanger. Would this be useful, and if so what format should it be in
(FTP server, Web pages, SRS database of parsers?) I would prefer to
set up web pages first as some versions of parsers may need wuite
detailed descriptions.

Such a repository could cover SRS5 and SRS6 parsers.  (Sorry, I really
do not fancy trying to support SRS4 any more :-)

Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/

More information about the Bio-srs mailing list

Send comments to us at archive@iubioarchive.bio.net