1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
|
<HTML>
<HEAD>
<TITLE>
EMBOSS: tfscan
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
tfscan
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Scans DNA sequences for transcription factors
<H2>
Description
</H2>
The <A HREF="http://www.gene-regulation.com/pub/databases.html">TRANSFAC
Database</A> is a commercial database of eukaryotic cis-acting
regulatory DNA elements and trans-acting factors. It covers the whole
range from yeast to human.
<p>
An old public domain version is available at:
<a href="ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z">
ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z</a>
<p>
The 'site.dat' data file from TRANSFAC contains information on individual
(putatively) regulatory protein binding sites. It has been divided into
the following taxonomic groups.
<p>
<ul>
<li>Fungi
<li>Insects
<li>Plants
<li>Vertebrates
<li>Other
</ul>
<p>
The program <b>tfscan</b> takes a sequence and the name of one of these
taxonomic groups and does a fast match of the TRANSFAC sequences against
the input sequence (optionally allowing mismatches).
<p>
The results is a list of the positions which match the binding sites in
the TRANSFAC SITE database.
<p>
Because the binding sites are so small, there will be many spurious
(false positive) matches.
<p>
<H2>
Usage
</H2>
<b>Here is a sample session with tfscan</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>tfscan </b>
Scans DNA sequences for transcription factors
Input nucleotide sequence(s): <b>tembl:k00650</b>
Transcription Factor Class
F : fungi
I : insect
P : plant
V : vertebrate
O : other
C : Custom
Select class [V]: <b>v</b>
Number of mismatches [0]: <b></b>
Output file [k00650.tfscan]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-menu menu [V] Select class (Values: F (fungi); I
(insect); P (plant); V (vertebrate); O
(other); C (Custom))
* -custom datafile Transfac database data file (optional)
-mismatch integer [0] Number of mismatches (Integer 0 or more)
[-outfile] outfile [*.tfscan] Output file name
Additional (Optional) qualifiers:
-minlength integer [1] Display matches equal to or above this
length (Integer 1 or more)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-menu</td>
<td>Select class</td>
<td><table><tr><td>F</td> <td><i>(fungi)</i></td></tr><tr><td>I</td> <td><i>(insect)</i></td></tr><tr><td>P</td> <td><i>(plant)</i></td></tr><tr><td>V</td> <td><i>(vertebrate)</i></td></tr><tr><td>O</td> <td><i>(other)</i></td></tr><tr><td>C</td> <td><i>(Custom)</i></td></tr></table></td>
<td>V</td>
</tr>
<tr>
<td>-custom</td>
<td>Transfac database data file (optional)</td>
<td>Data file</td>
<td><i>File in the data file path</i></td>
</tr>
<tr>
<td>-mismatch</td>
<td>Number of mismatches</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.tfscan</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-minlength</td>
<td>Display matches equal to or above this length</td>
<td>Integer 1 or more</td>
<td>1</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>tfscan</b> reads normal nucleic acid sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:k00650' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:k00650</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID K00650; SV 1; linear; genomic DNA; STD; HUM; 6210 BP.
XX
AC K00650; M16287;
XX
DT 26-JUL-1991 (Rel. 28, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 4)
XX
DE Human fos proto-oncogene (c-fos), complete cds.
XX
KW c-myc proto-oncogene; fos oncogene; proto-oncogene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-4165
RX PUBMED; 6574479.
RA van Straaten F., Muller R., Curran T., Van Beveren C., Verma I.M.;
RT "Complete nucleotide sequence of a human c-onc gene: deduced amino acid
RT sequence of the human c-fos protein";
RL Proc. Natl. Acad. Sci. U.S.A. 80(11):3183-3187(1983).
XX
RN [2]
RX DOI; 10.1016/0092-8674(85)90285-5.
RX PUBMED; 2414012.
RA Treisman R.;
RT "Transient accumulation of c-fos RNA following serum stimulation requires a
RT conserved 5' element and c-fos 3' sequences";
RL Cell 42(3):889-902(1985).
XX
RN [3]
RP 4166-6210
RX PUBMED; 3555978.
RA Verma I.M., Deschamps J., Van Beveren C., Sassone-Corsi P.;
RT "Human fos gene";
RL Cold Spring Harb. Symp. Quant. Biol. 51:0-0(0).
XX
DR EPD; EP11145; HS_FOS.
DR TRANSFAC; R00458; HS$CFOS_01.
DR TRANSFAC; R00459; HS$CFOS_02.
DR TRANSFAC; R00460; HS$CFOS_03.
DR TRANSFAC; R00461; HS$CFOS_04.
DR TRANSFAC; R00463; HS$CFOS_06.
DR TRANSFAC; R00464; HS$CFOS_07.
DR TRANSFAC; R00465; HS$CFOS_08.
DR TRANSFAC; R00466; HS$CFOS_09.
DR TRANSFAC; R00467; HS$CFOS_10.
DR TRANSFAC; R00468; HS$CFOS_11.
<font color=red> [Part of this file has been deleted for brevity]</font>
ccagctgtgc agctgcccac cgcaagggca gcagcagcaa tgagccttcc tctgactcgc 3300
tcagctcacc cacgctgctg gccctgtgag ggggcaggga aggggaggca gccggcaccc 3360
acaagtgcca ctgcccgagc tggtgcatta cagagaggag aaacacatct tccctagagg 3420
gttcctgtag acctagggag gaccttatct gtgcgtgaaa cacaccaggc tgtgggcctc 3480
aaggacttga aagcatccat gtgtggactc aagtccttac ctcttccgga gatgtagcaa 3540
aacgcatgga gtgtgtattg ttcccagtga cacttcagag agctggtagt tagtagcatg 3600
ttgagccagg cctgggtctg tgtctctttt ctctttctcc ttagtcttct catagcatta 3660
actaatctat tgggttcatt attggaatta acctggtgct ggatattttc aaattgtatc 3720
tagtgcagct gattttaaca ataactactg tgttcctggc aatagtgtgt tctgattaga 3780
aatgaccaat attatactaa gaaaagatac gactttattt tctggtagat agaaataaat 3840
agctatatcc atgtactgta gtttttcttc aacatcaatg ttcattgtaa tgttactgat 3900
catgcattgt tgaggtggtc tgaatgttct gacattaaca gttttccatg aaaacgtttt 3960
attgtgtttt taatttattt attaagatgg attctcagat atttatattt ttattttatt 4020
tttttctacc ttgaggtctt ttgacatgtg gaaagtgaat ttgaatgaaa aatttaagca 4080
ttgtttgctt attgttccaa gacattgtca ataaaagcat ttaagttgaa tgcgaccaac 4140
cttgtgctct tttcattctg gaagtcttgt aagtttctga aaggtattat tggagaccag 4200
tttgtcaaga agggtagctg ctggaggggg acacaccctc tgtctgatcc cttatcaaag 4260
aggacaagga aactatagag ctgattttag aatattttac aaatacatgc cttccattgg 4320
aatgctaaga ttttctactg cttctgggga cgggaaaccg ctgtgtaaca gcttttgtgg 4380
gaatacattt tttctgtttc agtactcgca gggggaaata tttaaatttt gttgtgctaa 4440
tattaaattc agatgttttg atcttaaagg aaccctttaa gcaaacagaa cctagctttg 4500
tacagactat tttaactttt tattctcaca aaatcacgtg gagggttatt ctacttcaaa 4560
gatgagcaaa ttgaagaatg gttagaataa acaactttct tgatattccg ttatcggcat 4620
tagaatcttc ctgctcgtta tcgtatccag caggctgaac tgcctcttga tacttggtta 4680
aaaaaaattt tcaggccggg cgcggtggcc catgcctgta atcctagcac tttgggaggc 4740
cgaggcaggc ggatcacctg aggtcgggag ttcgagacca gcctgaccaa catggagaaa 4800
ccccgtcttt actaaaaata caaaattagc ctggtgtggt ggtgcatgcc tgtaatccta 4860
gctacttgag aggctgagac aggaaaatca cttgaactcg ggaggcggat gttgcagcga 4920
actgagattg cgccattgca ctccagcctg ggcaacaaga ttgaaactct gtttaaaaaa 4980
aaaagttttc actaatgtgt acattttttt gtactctttt attctcgaaa gggaaggagg 5040
gctattgccc tatcccttat taataaatgc attgtggttt ctggtttctc taataccata 5100
tgcccttcat tcagtttata gtgggcggaa gtgggggaga aaaagttgct cagaaatcaa 5160
aagatatctc aaacagcaca aataatggct gatcgttctg caaacaaaaa gttacataat 5220
agctcaagaa ggagaagtca acatgactct gaacaagctt taacttagaa actttatcat 5280
cttaaggaag aacgtgacct ttgtccagga cgtctctggt aatggggcac ttacacacac 5340
atgcacacgt acaaaccaca gggaaaggag accgcccttc tgcctctgct cgcgagtatc 5400
acgcaggcac catgcactat gttttcacac acactgggtg gaagaagagc ttcagcgcca 5460
gtcttctaat gctttggtga taatgaaaat cactgggtgc ttatggggtg tcatattcaa 5520
tcgagttaaa agttttaatt caaaatgaca gttttactga ggttgatgtt ctcgtctatg 5580
atatctctgc ccctcccata aaaatggaca tttaaaagca acttaccgct ctttagatca 5640
ctcctatatc acacaccact tggggtgctg tttctgctag acttgtgatg acagtggcct 5700
taggatccct gtttgctgtt caaagggcaa atattttata gcctttaaat atacctaaac 5760
taaatacaga attaatataa ctaacaaaca cctggtctga aataacaagg tgatctaccc 5820
tggaaggaac ccagctggtg ggccaggagc ggtggctcac acctgtaatt ccagcacttt 5880
gggaggctga gacaggagga tcactggagt ccaggagttt gagaccagcc tgggcaacat 5940
ggcaaaaccc agtgtgcttc tgttgtccca gctacactac tcaggaggct gaggcaggag 6000
tatgacttga gcctgggagg gggaggttgc agagaactga tattgcacca ccactgcact 6060
ccagcctggg tgacacagca aaaccctatc tcaaaaaaaa aaaaaaaaaa aaggaaccca 6120
gctggttcct gtaggtgtgc aataataaca accagaggaa gaaaaggaag acgatttccc 6180
agatgaagaa gggcagctgg accttcggac 6210
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: k00650.tfscan</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
TFSCAN of K00650 from 1 to 6210
MOUSE$FCGR3A_02 R04413 3287 3292 ttcctc
T00702; PU.1;Quality: 3; Species: mouse, Mus musculus.
HS$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
T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus.
HS$ALBU_02 R00078 2009 2014 ttggca
</pre>
</td></tr></table><p>
<p>
The output consists of a title line then 5 columns separated by whitespace.
<p>
The first column is the identifier of the entry.
<p>
The second column is the Accession Number of the entry.
<p>
The third and fourth columns are the start and end positions of the
match in your input sequence.
<p>
The fifth column is the sequence of the region where a match has been found.
<p>
Binding factor information, where available, is given at the end
of the matches for each matching entry.
<H2>
Data files
</H2>
<b>tfscan</b> reads the TRANSFAC SITE data held in the EMBOSS data files:
<p>
<ul>
<li>tffungi
<li>tfinsect
<li>tfplant
<li>tfvertebrate
<li>tfother
</ul>
<p>
Your EMBOSS administrator will have to run the EMBOSS program <b>tfextract</b>
in order to set these files up from the TRANSFAC distribution files.
<p>
<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ul>
<li>Nucleic Acids Res. 16: 1879-1902, 1988
<li>BioTechForum - Advances in Molecular Genetics
(J. Collins,A.J. Driesel, eds.) 4:95-108, 1991
<li>Nucleic Acids Res. 20:3-26, 1992
</ul>
<H2>
Warnings
</H2>
Your EMBOSS administrator will have to run the EMBOSS program <b>tfextract</b>
in order to set up the data files from the TRANSFAC distribution files.
<p>
<H2>
Diagnostic Error Messages
</H2>
"EMBOSS An error in tfscan.c at line 82:
<br>
Either EMBOSS_DATA undefined or TFEXTRACT needs running"
<p>
This means that you should contact your EMBOSS administrator and ask
them to run the <b>tfextract</b> program to set up the TRANSFAC data for
EMBOSS.
<p>
<H2>
Exit status
</H2>
It always exits with a status of 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
</table>
<p>
Your EMBOSS administrator will have to run the EMBOSS program <b>tfextract</b>
in order to set up the data files from the TRANSFAC distribution files.
<p>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written Summer 2000 - Alan Bleasby
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
|
