Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/~megabotan/term6/gibbs_m_200_o.txt Дата изменения: Wed May 30 16:50:28 2012 Дата индексирования: Mon Oct 1 22:11:36 2012 Кодировка: Поисковые слова: m 8

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/tmp/gibbs9135/Gibbs9135 /tmp/gibbs9135/data.txt 16 20 -n -r -W 0.8 -w 0.1 -p 200 -j 5 -i 2000 -S 40 -C 0.5 -P /tmp/gibbs9135/prior.txt -R 1,1,8 -U /tmp/gibbs9135/spacing.txt -M 1,24 -B /tmp/gibbs9135/data.txt_info-det -y -nopt -o /tmp/gibbs9135/outfile.txt


Gibbs 3.10.001 Sep 8 2009
Data file: /tmp/gibbs9135/data.txt
Output file: /tmp/gibbs9135/outfile.txt
Priors file: /tmp/gibbs9135/prior.txt
Background Composition Model file: /tmp/gibbs9135/data.txt_info-det
Spacing Model file: /tmp/gibbs9135/spacing.txt
Current directory: /tmp/gibbs9135
The following options are set:
Concentrated Region False Sequence type False
Collapsed Alphabet False Pseudocount weight True
Use Expectation/Maximization False Don't Xnu sequence False
Help flag False Near optimal cutoff True
Number of iterations True Don't fragment False
Don't use map maximization False Repeat regions False
Output file True Informed priors file True
Plateau periods True palindromic sequence True
Don't Reverse complement True Number of seeds True
Seed Value False Pseudosite weight True
Suboptimal sampler output False Overlap False
Allow width to vary False Wilcoxon signed rank False
Sample along length False Output Scan File False
Output prior file False Modular Sampler False
Ignore Spacing Model False Sample Background False
Bkgnd Comp Model True Init from prior False
Homologous Seq pairs False Parallel Tempering False
Group Sampler False No progress info False
Fragment from middle False Verify Mode False
Alternate sample on k False No freq. soln. True
Calc. def. pseudo wt. False Motif/Recur smpl False
Phylogenetic Sampling False Supress Near Opt. True
Nearopt display cutoff False Sample model False
Hierarchical Model False Centroid model False
Print Bayesian Counts False Align Centroid False
Calculate Credibility Limits False Frequency Bkgnd. False

site_samp = 0
nMotifLen = 16
nAlphaLen = 4
nNumMotifs = 20
dPseudoCntWt = 0.1
dPseudoSiteWt = 0.8
nMaxIterations = 2000
lSeedVal = 1338374657
nPlateauPeriods = 200
nSeeds = 40
nNumMotifTypes = 1
dCutoff = 0.5
dNearOptDispCutoff = 0.5
RevComplement = 0
glOverlapParam = 0
Rcutoff factor = 0
Post Plateau Samples = 0
Frag/Shft Per. = 5
Frag width = 24


Sequences to be Searched:
_________________________
#1 pheA
#2 aroH2
#3 tyrB
#4 aroKB2
#5 aroKB1
#6 aroF+tyrA
#7 aroA
#8 aroL
#9 aroC
#10 aroG
#11 aroD+ydiB
Processed Sequence Length: 2200 Total sequence length: 2200










======================================================================
======================== MAP MAXIMIZATION RESULTS ====================
======================================================================

-------------------------------------------------------------------------
MOTIF a





Motif model (residue frequency x 100)
____________________________________________
Pos. # a t c g Info
_____________________________
1 | 71 . 28 . 0.6
2 | 42 . 28 28 0.2
3 | 71 28 . . 0.5
4 | 14 . . 85 0.8
5 | 14 . 42 42 0.4
6 | 85 . . 14 0.7
7 | 42 14 14 28 0.1
8 | . 100 . . 0.9
9 | 100 . . . 1.0
10 | 42 28 . 28 0.2
11 | . 100 . . 0.9
12 | . . 57 42 0.6
13 | . 42 57 . 0.5
14 | 28 57 . 14 0.2
15 | . 85 . 14 0.7
16 | . 85 . 14 0.7

nonsite 26 29 20 22
site 32 33 14 19

Motif probability model
____________________________________________
Pos. # a t c g
____________________________________________
1 | 0.615 0.065 0.269 0.051
2 | 0.393 0.065 0.269 0.273
3 | 0.615 0.288 0.046 0.051
4 | 0.171 0.065 0.046 0.718
5 | 0.171 0.065 0.380 0.384
6 | 0.726 0.065 0.046 0.162
7 | 0.393 0.177 0.157 0.273
8 | 0.059 0.843 0.046 0.051
9 | 0.837 0.065 0.046 0.051
10 | 0.393 0.288 0.046 0.273
11 | 0.059 0.843 0.046 0.051
12 | 0.059 0.065 0.491 0.384
13 | 0.059 0.399 0.491 0.051
14 | 0.282 0.510 0.046 0.162
15 | 0.059 0.732 0.046 0.162
16 | 0.059 0.732 0.046 0.162



Background probability model
0.264 0.292 0.212 0.231



16 columns
Num Motifs: 7
1, 1 108 gttga AGAAGAGTAGTCCTTT atatt 123 0.63 F pheA
2, 1 94 gtact AGAGAACTAGTGCATT agctt 109 0.60 F aroH2
4, 1 125 ccgta AAAGCGGTAATGTTTT tacgc 140 0.69 F aroKB2
7, 1 185 tagcc ACAGGAATAATGTATT 200 0.77 F aroA
10, 1 134 taatt CCAGGATTAATCCGTT catag 149 0.74 F aroG
11, 1 76 tgggt AATGCAATATTCTTTT caggt 91 0.79 F aroD+ydiB
11, 2 170 tatga CATGCAATATTCCTGG aaaca 185 0.74 F aroD+ydiB
****************


Column 1 : Sequence Number, Site Number
Column 2 : Left End Location
Column 4 : Motif Element
Column 6 : Right End Location
Column 7 : Probability of Element
Column 8 : Forward Motif (F) or Reverse Complement (R)
Column 9 : Sequence Description from Fast A input

Log Motif portion of MAP for motif a = -111.01453
Log Fragmentation portion of MAP for motif a = -0.00000


Log Background portion of Map = -2890.25793
Log Alignment portion of Map = -51.53751
Log Site/seq portion of Map = 0.00000
Log Null Map = -3044.34747
Non Palindromic Map = -16.04418
Log Map = -8.46250


log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null

Frequency Map = -8.462502
Nearopt Map = -8.462502
Maximal Map = -8.462502
Elapsed time: 16.470000 secs