where to download transfac data file?

clwu newgene at bigfoot.com
Thu Feb 6 17:00:50 UTC 2003


Thank you, folks,
                I downloaded the transfac ver3.2. I extracted it out to 
EMBOSS data file and ran "tfextract". "tfscan" ran OK now, but the 
output is different with the tfscan's document. No pattern name shown in 
my result. That is hard to intepret the result. I suspect it's the 
format problem of database file. My emboss (ver2.51)  is built on 
cygwin/win2000. And the first several lines of my "tfvertebrate" is 
"HS$6-16_01\r          gGGAAAaTGAAACT R00001\nHS$6-16_02\r          
GGGGAAAATGAAACTGCA R00002\n" (invisible chars are escaped)
                If it is the problem, what's the correct format?

Thanks again,

Cl Wu

 >>>>mine<<<<
TFSCAN of HUMFOS from 1 to 6210

  3287  3292  ttcctc
  4045  4050  catgtg
  3498  3503  catgtg
  5590  5593  cccc
  4801  4804  cccc
  3239  3242  cccc
  3221  3224  cccc
  3150  3153  cccc
  2881  2884  cccc
  2089  2092  cccc
  1941  1944  cccc

 >>>>tfscan's doc<<<
TFSCAN of HSFOS from 1 to 6210

MOUSE$FCGR3A_02      R04413   3287  3292  ttcctc
HS$ALBU_03           R00079   5940  5944  tggca
HS$ALBU_03           R00079   3757  3761  tggca
HS$ALBU_03           R00079   2776  2780  tggca
HS$ALBU_03           R00079   2418  2422  tggca
HS$ALBU_03           R00079   2010  2014  tggca
HS$ALBU_03           R00079   1676  1680  tggca
HS$ALBU_03           R00079   1356  1360  tggca
HS$ALBU_02           R00078   2009  2014  ttggca




Bhattacharyya, Pranay wrote:

>Sorry.
>This one seems to be a newer version than the one I previously sent you.
>ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z
>
>version 3.3 and 3.4 doesn't look to be available from their website.
>I wonder why they removed it.
>
>Hope this helps.
>
>Pranay
>
>-----Original Message-----
>From: clwu [mailto:newgene at bigfoot.com]
>Sent: Wednesday, February 05, 2003 5:23 PM
>To: emboss at embnet.org
>Subject: where to download transfac data file?
>
>
>Hi, group,
>              EMBOSS tool "tfscan" needs TRANSFAC database. However when 
>I tried to download it following the link in tfextract document:
>       
>http://transfac.gbf.de/cgi-bin/download/download.pl
>
>I couldn't download it because I don't have the permission.
>
>I counld not find it neither from their ftp server: 
>ftp://transfac.gbf.de/pub/ .
>
>Help, please.
>
>Thank you.
>
>
>Cl Wu
>  
>






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