Web Output

Results can be displayed online or sent to you by email depending on your options. The default is to email your result. To display online result, you need to register.

If online display, a sequence logo (single- or two-block) is generated on the fly, for example, see the crp seq logos. The sequence logo is generated using seqlogo.pl from WegLogo software of UC Berkeley. If it is bipartite logo, a gap histogram is generated on the fly also. In addition, a motif table is printed (as an example, see the table below). The table prints sequence names in the first column and the rest are read from the bipad output (in motif part).

If results output via email (default), bipad-mailer sends your output text file only. Please do not reply, since it is by auto-mailing program. If you need plotting sequence logos, you have to select result display on-line.

Attention: there is a web server timeout. If your project run out of time, you won't see your result online. But you can download your results later on, whereas you need to remember your job ID number assigned in each run. In this case we recommend you select your results sent by email rather than print online. Replace the "ID" in the following links with your assigned job number and get your files.

Locations of downloadable files:
    Your DNA sequence file: http://bipad.cmh.edu/dnaseqID
    Your output file: http://bipad.cmh.edu/bipadoutID
    Sequence logo file: http://bipad.cmh.edu/bipadoutID.png
    Gap histogram file: http://bipad.cmh.edu/histogramID.png

A bipartite logo (as shown in the figure below) is produced by inserting a fixed 5-bp gap (position 0-4) in between two one-block motif logos instead of predominant gap size due to the limited picture width. The central gap size and gap distribution are reported in the bipad output file for your download.

If your result option is by email, then after you click on "Bipad Search" button, you will receive an email from us shortly that containing your results. it usually takes several seconds to minutes to send your results depending on how large your project is.

  Download Output Files
Bipad output file (see crp example below) and sequence logo file are available for download.

  Single-Block Motif Logo

  Bipartite Motif Logo

  Gap Histogram

  Motif Table

Sequence	No.	Strand	5'	flank	Motif1	flank	3'	Ri	Gap	Strand	5'	flank	Motif2	flank	3'	Ri	Comb_Ri(bits)
CE1CG	1	(+)	60	tgt	TTTTTTGA	tcg	67	7.537	6	(+)	74	ttt	TCACAAAA	atg	81	6.906	14.442
ECOARABOP	2	(+)	54	tga	TTATTTGC	acg	61	4.038	6	(+)	68	gcg	TCACACTT	tgc	75	10.130	14.168
ECOBGLR1	3	(+)	75	aat	AACTGTGA	gca	82	7.890	6	(+)	89	tgg	TCATATTT	tta	96	7.488	15.378
ECOCRP	4	(+)	60	tgc	ATGTATGC	aaa	67	4.252	8	(+)	76	acg	TCACATTA	ccg	83	9.158	13.409
ECOCYA	5	(+)	49	gca	AGGTGTTA	aat	56	4.652	6	(+)	63	tga	TCACGTTT	tag	70	7.196	11.848
ECODEOP2	6	(+)	6	gaa	TTATTTGA	acc	13	6.226	6	(+)	20	aga	TCGCATTA	cag	27	5.674	11.900
ECOGALE	7	(+)	43	cta	ATTTATTC	cat	50	2.494	4	(+)	55	atg	TCACACTT	ttc	62	10.130	12.624
ECOILVBPR	8	(+)	38	aca	AAACGTGA	tca	45	6.174	8	(+)	54	ccc	TCAATTTT	ccc	61	5.584	11.757
ECOLAC	9	(+)	80	tgg	AATTGTGA	gcg	87	9.201	5	(+)	93	gga	TAACAATT	tca	100	6.173	15.375
ECOMALE	10	(+)	13	caa	TTCTGTAA	cag	20	4.617	6	(+)	27	aga	TCACACAA	agc	34	7.203	11.820
ECOMALK	11	(+)	60	gaa	TTTCGTGA	tgt	67	7.695	8	(+)	76	ctt	GCAAAAAT	cgt	83	5.702	13.398
ECOMALT	12	(+)	40	tgg	AATTGTGA	cac	47	9.201	6	(+)	54	agt	GCAAATTC	aga	61	4.672	13.874
ECOOMPA	13	(+)	47	cat	ATGCCTGA	cgg	54	3.935	6	(+)	61	agt	TCACACTT	gta	68	10.130	14.064
ECOTNAA	14	(+)	70	aac	GATTGTGA	ttc	77	6.432	6	(+)	84	gat	TCACATTT	aaa	91	10.770	17.201
ECOUXU1	15	(+)	16	aat	TGTTGTGA	tgt	23	7.937	8	(+)	32	tta	ACCCAATT	aga	39	3.968	11.906
PBR322	16	(+)	52	atg	CGGTGTGA	aat	59	4.577	6	(+)	66	acc	GCACAGAT	gcg	73	5.645	10.222
TRN9CAT	17	(+)	52	tga	TACCGGGA	agc	59	2.168	8	(+)	68	tgg	GCCAACTT	ttg	75	4.620	6.788
TDC	18	(+)	77	tta	ATTTGTGA	gtg	84	9.758	6	(+)	91	gtc	GCACATAT	cct	98	8.251	18.009

* Rseq( left) = 6.04351 bits ( 0.75544 bits per base)
* Rseq(right) = 7.18884 bits ( 0.89860 bits per base)

Your results are kept in our server for one day.

Example result by searching CRP binding sites

Sample options

• two-block search pattern: 8<[3, 9]>8
• alignment mode: forward strand
• cycles: 400
• flanking bases: 3, 3 (bps)

Sample output from bipad server

* From: Bipad Server at Children's Mercy Hosp. at Kansas City, MO

  + jobID: 20040825171630
  + Email: cpbi@psualum.com
  + Submission date: Wed Aug 25 17:16:30 CDT 2004
  + Client: 63.78.74.228
  + Project: CRP binding sites

* Bipartite Pattern Discovery, BIPAD v0.10, (C)2003-2005 CMH
* Bipad program was written in C++ by Dr. Chengpeng Bi (cbi@cmh.edu)
* ================================================================================

* Sequence Model: OOPS
* Search pattern: Two-block (8<[3, 9]>8) on forward strand
* Sequence file: dnaseq20040825171630.fa
* Output file: bipadout20040825171630
* Bipad parameters:  -T 'CRP binding sites'  -1  -y 400  -k 3 -j 3  -2Dd -l 8 -m 8 -a 3 -b 9  -is 
*
* Sequence no.	vs	 its name
*	1	==>	CE1CG
*	2	==>	ECOARABOP
*	3	==>	ECOBGLR1
*	4	==>	ECOCRP
*	5	==>	ECOCYA
*	6	==>	ECODEOP2
*	7	==>	ECOGALE
*	8	==>	ECOILVBPR
*	9	==>	ECOLAC
*	10	==>	ECOMALE
*	11	==>	ECOMALK
*	12	==>	ECOMALT
*	13	==>	ECOOMPA
*	14	==>	ECOTNAA
*	15	==>	ECOUXU1
*	16	==>	PBR322
*	17	==>	TRN9CAT
*	18	==>	TDC      
*

Bipartite Pattern Discovery, BIPAD v0.10, (C)2003-2005
Project title: CRP binding sites
Sequence file: ../html/output/dnaseq20040825171630.fa.txt
command-line: ./bipad -T CRP binding sites -1 -y 400 -k 3 -j 3 -2Dd -l 8 -m 8 -a 3 -b 9 -is ../html/output/dnaseq20040825171630.fa.txt
Project start: Wed Aug 25 17:16:30 2004

Residue composition in the sequence set:
	A = 0.30265 (572) | C = 0.18254 (345) | G = 0.20899 (395) | T = 0.30582 (578)
	Total bases: 1890 (Nn = 0)
Number of sequences (N): 18
Maximum oligo length (Lmax): 105
Number of Monte Carlo cycles: 400
Alignment Mode: forward strand only
pseudocounts: 1.5
number of flanking bases: 3
Left  motif length (J1): 8 bps
Searching method (J1): Greedy algorithm
Right motif length (J2): 8 bps
Searching method (J2): Greedy algorithm
gap range: 3, 9
min_H = 19.343 (bits)
Total iterations: 42300
Best alignment in cycle 280

* Motif Model for Left-half Sites
* motif length =  8
*
* information weight matrix
*	 Ri(a,l)	 Ri(c,l)	 Ri(g,l)	 Ri(t,l)	 l	  a	  c	  g	  t
	       0	       7	frombase, tobase
	 0.82319	-1.94620	-1.94620	 0.47702	 0	  9	  1	  1	  7
	 0.26680	-3.82066	-0.65074	 0.82319	 1	  6	  0	  3	  9
	-0.65074	-0.65074	-0.27634	 0.66046	 2	  3	  3	  4	  8
	-3.82066	-0.27634	-3.82066	 1.43986	 3	  0	  4	  0	 14
	-1.15770	-1.94620	 1.22373	-0.65074	 4	  2	  1	 12	  3
	-3.82066	-3.82066	-1.94620	 1.71331	 5	  0	  0	  1	 17
	-1.94620	-3.82066	 1.53689	-1.15770	 6	  1	  0	 15	  2
	 1.53689	-0.65074	-3.82066	-3.82066	 7	 15	  3	  0	  0
*
	 6.04351 bits = mean (Rsequence of selected region)
	 2.31757 bits = standard deviation
*

* Motif Model for Right-half Sites
* motif length =  8
*
* information weight matrix
*	 Ri(a,l)	 Ri(c,l)	 Ri(g,l)	 Ri(t,l)	 l	  a	  c	  g	  t
	       0	       7	frombase, tobase
	-1.94620	-3.82066	 0.02064	 1.22373	 0	  1	  0	  5	 12
	-1.94620	 1.71331	-3.82066	-3.82066	 1	  1	 17	  0	  0
	 1.53689	-1.15770	-1.94620	-3.82066	 2	 15	  2	  1	  0
	-0.27634	 1.33584	-3.82066	-1.94620	 3	  4	 13	  0	  1
	 1.62780	-3.82066	-1.94620	-1.94620	 4	 16	  0	  1	  1
	-0.27634	 0.02064	-1.94620	 0.66046	 5	  4	  5	  1	  8
	 0.02064	-3.82066	-3.82066	 1.33584	 6	  5	  0	  0	 13
	-0.27634	-1.94620	-3.82066	 1.33584	 7	  4	  1	  0	 13
*
	 7.18884 bits = mean (Rsequence of selected region)
	 2.13850 bits = standard deviation
*
* gap distance distribution
distance	frequency
       0	       0
       1	       0
       2	       0
       3	       0
       4	       1
       5	       1
       6	      11
       7	       0
       8	       5
       9	       0
gap center:   6
*
* Bipartite Motif Model for CRP binding sites
* Pattern: M1<d>M2
* Penalty: disabled
* Column  1: sequence number [1 --  18]
* Left Motif Model (M1):
* 	Motif Size (J1) =   8 bps
* 	Column  2: strand attribute(+/-)
* 	Column  3: motif start position [0, 97]
* 	Column  4: motif string (oligos)
* 	Column  3: motif end position [7, 104]
* 	Column  5: Ri value (bits)
* Column 6: gap  between motifs (bps)
* Right Motif Model (M2):
* 	Motif Size (J2) =   8 bps
* 	Column  7: strand attribute(+/-)
* 	Column  8: motif start position [0, 97]
* 	Column  9: motif string (oligos)
* 	Column 10: motif end position [7, 104]
* 	Column 11: Ri value (bits)
* Column 12: combined Ri (left + right - gap_penalty), comb_Ri
   1	 (+)  60 tgt TTTTTTGA tcg 67      7.537  <  6>  (+)  74 ttt TCACAAAA atg 81      6.906   14.442
   2	 (+)  54 tga TTATTTGC acg 61      4.038  <  6>  (+)  68 gcg TCACACTT tgc 75     10.130   14.168
   3	 (+)  75 aat AACTGTGA gca 82      7.890  <  6>  (+)  89 tgg TCATATTT tta 96      7.488   15.378
   4	 (+)  60 tgc ATGTATGC aaa 67      4.252  <  8>  (+)  76 acg TCACATTA ccg 83      9.158   13.409
   5	 (+)  49 gca AGGTGTTA aat 56      4.652  <  6>  (+)  63 tga TCACGTTT tag 70      7.196   11.848
   6	 (+)   6 gaa TTATTTGA acc 13      6.226  <  6>  (+)  20 aga TCGCATTA cag 27      5.674   11.900
   7	 (+)  43 cta ATTTATTC cat 50      2.494  <  4>  (+)  55 atg TCACACTT ttc 62     10.130   12.624
   8	 (+)  38 aca AAACGTGA tca 45      6.174  <  8>  (+)  54 ccc TCAATTTT ccc 61      5.584   11.757
   9	 (+)  80 tgg AATTGTGA gcg 87      9.201  <  5>  (+)  93 gga TAACAATT tca 100     6.173   15.375
  10	 (+)  13 caa TTCTGTAA cag 20      4.617  <  6>  (+)  27 aga TCACACAA agc 34      7.203   11.820
  11	 (+)  60 gaa TTTCGTGA tgt 67      7.695  <  8>  (+)  76 ctt GCAAAAAT cgt 83      5.702   13.398
  12	 (+)  40 tgg AATTGTGA cac 47      9.201  <  6>  (+)  54 agt GCAAATTC aga 61      4.672   13.874
  13	 (+)  47 cat ATGCCTGA cgg 54      3.935  <  6>  (+)  61 agt TCACACTT gta 68     10.130   14.064
  14	 (+)  70 aac GATTGTGA ttc 77      6.432  <  6>  (+)  84 gat TCACATTT aaa 91     10.770   17.201
  15	 (+)  16 aat TGTTGTGA tgt 23      7.937  <  8>  (+)  32 tta ACCCAATT aga 39      3.968   11.906
  16	 (+)  52 atg CGGTGTGA aat 59      4.577  <  6>  (+)  66 acc GCACAGAT gcg 73      5.645   10.222
  17	 (+)  52 tga TACCGGGA agc 59      2.168  <  8>  (+)  68 tgg GCCAACTT ttg 75      4.620    6.788
  18	 (+)  77 tta ATTTGTGA gtg 84      9.758  <  6>  (+)  91 gtc GCACATAT cct 98      8.251   18.009
*
* Rseq( left) =  6.04351 bits ( 0.75544 bits per base)
* Rseq(right) =  7.18884 bits ( 0.89860 bits per base)

* Sequence Logo for CRP binding sites
* Bipartite model (left- + right-half)
* position, number of sequences, information Rs, variance of Rs
4 number of symbols in DNA or RNA
 -6	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
 -5	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
 -4	 18	0.380858	0.020337
a	  9
c	  1
g	  1
t	  7
 -3	 18	0.392072	0.012820
a	  6
c	  0
g	  3
t	  9
 -2	 18	0.015216	0.014385
a	  3
c	  3
g	  4
t	  8
 -1	 18	1.058484	0.017305
a	  0
c	  4
g	  0
t	 14
  0	 18	0.470608	0.026644
a	  2
c	  1
g	 12
t	  3
  1	 18	1.510008	0.020331
a	  0
c	  0
g	  1
t	 17
  2	 18	1.043985	0.026984
a	  1
c	  0
g	 15
t	  2
  3	 18	1.172283	0.019773
a	 15
c	  3
g	  0
t	  0
  4	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
  5	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
  6	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
  7	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
  8	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
  9	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
 10	 18	0.713431	0.020291
a	  1
c	  0
g	  5
t	 12
 11	 18	1.510008	0.020331
a	  1
c	 17
g	  0
t	  0
 12	 18	1.043985	0.026984
a	 15
c	  2
g	  1
t	  0
 13	 18	0.795242	0.022801
a	  4
c	 13
g	  0
t	  1
 14	 18	1.230686	0.027242
a	 16
c	  0
g	  1
t	  1
 15	 18	0.129740	0.015426
a	  4
c	  5
g	  1
t	  8
 16	 18	0.970506	0.014287
a	  5
c	  0
g	  0
t	 13
 17	 18	0.795242	0.022801
a	  4
c	  1
g	  0
t	 13
 18	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4
 19	 16	0.000000	0.000000
a	  4
c	  4
g	  4
t	  4

Project completion time = 25 seconds