tfscan

[Lakshmanan Iyer]

Hello,
You are right! The latest versions are provided by BioBase. Cognia Inc. is
the exclusive North American distribution of database products from BIOBASE
(http://www.cognia.com). I know this for sure because right now I am dealing
with them. 
Lakshmanan Iyer, Ph. D.
Computational Biologist
Manager of Collaboration and Training
Computational Biology Group
Bauer Center for Genomics Research
Bauer Laboratory
7 Divinity Ave.
Cambridge, MA 02138
www.cgr.harvard.edu
Phone:617-384-7647
Fax: 617-495-2196

-----Original Message-----
From: Michael Black [mailto:mbb8n at virginia.edu] 
Sent: Thursday, July 10, 2003 12:40 PM
To: emboss at embnet.org
Subject: RE: tfscan

It was my understanding that as of a year or so ago (or two now ? I 
can't remember when the notice came out), there is no such thing as a 
freely downloadable TRANSFAC database.  If you want the latest version, 
you must pay for it, through BioBase Corporation or their US 
distributors, Cognia Corp.  Of course, there are free web portals to 
BioBase's products (www.gene-regulation.com), just no free downloads 
for local use.

If I'm wrong, someone will hopefully post a URL or FTP address, but I 
remember getting an email a long time ago from BioBase, when they took 
over the database, that it would no longer be freely distributed.

Cheers, Michael
_________________________________
Michael B. Black, Ph.D.
Molecular Biology Computing Support
Univ. of Virginia, ITC-ACHS
_________________________________



On Thursday, July 10, 2003, at 01:02  PM, Lapointe, David wrote:

> I have noticed this also and I have had others complain about this.
>
> Related to this question is where one gets the public version of the
> database (containing site.dat)? It should be version 6 by now.
>
> David
>
>
>> -----Original Message-----
>> From: peter robinson [mailto:Peter.Robinson at t-online.de]
>> Sent: Friday, July 11, 2003 3:46 AM
>> To: emboss at embnet.org
>> Subject: tfscan
>>
>>
>> Hi EMBOSSers,
>>
>> I have just set up a transfac database on my site with
>> tfextract and then
>> tried out tfscan for the first time. I was suprised to see
>> lots and lots of
>> trivial hits of 2nt in length mixed in with matches that
>> appeared more
>> believable. My input was a file with about 100 FASTA
>> sequences of putative
>> upstream conserved regions, and I otherwise used the default settings.
>>
>> What's going on? Is it possible to have tfscan just return
>> hits greater than a
>> certain length (didn't see anything like that in the documentation)?
>>
>> Thanks
>>
>> Peter Robinson
>>
>>