Fwd: Re: Suggestion for new use for EMBOSS program

Per Johansson heme at postmark.net
Thu Nov 7 15:11:43 UTC 2002

It's OK to reformat the GCG pattern file to a transfac-format database
and use tfscan. But I still miss some functions in FINDPATTERNS. I
can't search the reverse primer strand, the output is limited to ONE
format no alignment format, tfscan it doesn't accept wobbeling bases
in primers (e.g. K=G or T , D=G or C or A not-T ...). But otherwise
the tfscan algorithm is a very nice and fast word-matching algorithm,
but it COULD be used for other purposes also! 


--- Forwarded Message ---
To: EMBOSS <emboss at embnet.org>
From: Charles Plessy <charles at moulinette.dyndns.org>
Reply-To: c.plessy at mangoosta.net
Subject: Re: Suggestion for new use for EMBOSS program
Date: Thu, 7 Nov 2002 14:20:42 +0100

> The best replacement I've found is the EMBOSS program tfscan!

> Obviously, I could write a script to wrap tfscan but I'd like to
> avoid this.  A new program with this functionality would be beneficial
> for the EMBOSS package.

An alternative would be to write a script that builds a
transfac-format database from a flatfile containing names and
corresponding consensus (This would also allow to migrate the
pattern.dat file of GCG).


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