Dear Fergus
You can also use the EMBOSS programs fuzzpro or patmatmotifs which both
accept a protein motif and searches one or more protein sequences, or a
protein sequence database. To search a database enter database_name:*, for
example sw:* is swissprot. See the help for details.
http://www.uk.embnet.org/Software/EMBOSS/.
A list of web interface to EMBOSS are available at
http://www.uk.embnet.org/Software/EMBOSS/general.html, and include David
Bauer's implemtation of the PISE web interface at
http://ubigcg.mdh4.mdc-berlin.de:8080/emboss.html.
You can also use access EMBOSS if you have an account with the HGMP
www.hgmp.mrc.ac.uk.
Best wishes
Aedin Culhane
