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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