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Transfac databases

Nick Staffa Staffa at NIEHS.NIH.GOV
Fri Mar 29 09:58:58 EST 1996


I am gratified that someone at Transfac answered my mail toot sweet.
I have responded to him again asking that he please answer my 
question. Since he also posted to info-gcg, I now take the liberty
to ask you all if this is really an answer to my question or a bit
of ridicule of what I would like to do.  I know that I am a bit
sensitive to any question of the "why would you want to do that" sort,
but don't see how MatInspector is going to search genbank. Even if it
would, it would be courteous to have answered the question.

Several years ago when I was evaluating balances for animal weighing,
I had occasion to talk to the Mettler people in Switzerland. I got the
same arrogant attitude: what do you want to do that for.  That time it
might have been defensive since their high-priced balance could not
be made to do what a much cheaper balance did quite well. 

So I wonder, is this a European trait?

From:   IN%"frech at gsf.de"  "Kornelie Frech"
To:     IN%"Staffa at NIEHS.NIH.GOV"
CC:
Subj:   RE: Transfac databases


Staffa at NIEHS.NIH.GOV (Nick Staffa) wrote:
>(This is my second posting using netscape mail service, since I do not 
>see my first neither on the info-gcg web page nor in my mailbox)
>
>I have been exploring the site 
>http://transfac.gbf-braunschweig.de/TRANSFAC/browse.html
>They maintain a database of profiles of transcription binding sites
>along with other data.  I am interested in this because I would 
>like to do a profilesearch using profiles of binding sites.
>The profiles that  Transfac gives are not acceptable to GCG.
>If I could get at the aligned sequences that were used to generate
>the profiles at Transfac, or even the raw sequences in an IG file,
>I could create my own GCG profiles with profilemake.
>Although these files are alluded to, I could not discover them after
>many hours of searching. I thought they might be included in the
>download of MatInspector,but all I found was one or two examples.
>
>Does anyone know how to get at the aligned sequence files used to 
>create the profiles at Transfac?

>>>>>Kornelie Frech Replied:
Why do want to create your own profiles? The program MatInspector does 
exactly
what you want. It locates matches to transcription factor binding 
sites in
nucleotide sequences of unlimited length. 
The GCG programs profilemake and profilesearch are developed for 
protein
sequence analysis. In the GCG manual is stated, that they have little
experience using nucleotide sequences with profile analysis.


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