DATABASE SEARCH RESULTS ALIGNMENTS MOTIF DIAGRAMS EXPLANATION OF OUTPUT PROGRAM PARAMETERS


The MEME Suite of motif-based sequence analysis tools.



version 4.6.1 (Release date: 8 EST 20)

Program: mhmmscan
File contents: Database search results
Motif file: crp0.meme.html
HMM file: mcast_out/crp0.meme.html.mhmm
Sequence file: crp0.fasta
Create date: Tue Jun  7 15:29:50 2011


For further information on how to interpret these results or to get a copy of the MEME Suite software, please access http://meme.sdsc.edu.

If you use this program in your research, please cite

William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Meta-MEME: Motif-based hidden Markov models of protein families." Computer Applications in the Biosciences. 13(4):397-406, 1997.


DATABASE SEARCH RESULTS

IDE-valueScoreHitsSpanStartEndDescription
lacnan20.55235943
trn9catnan13.7126636101
ilvnan12.71256560
aranan9.701185976
malenan9.422351448
maltnan9.281184158
deop2nan8.461186077
pbr322nan7.291185774
uxu1nan6.941181734
ce1cgnan6.581186582
tnaanan5.901187592
galenan5.901184663
cyanan5.361185067
crpnan5.251186784
ompanan4.741184865
malknan4.741186178
tdcnan4.441188299



ALIGNMENTS

ID
E-value
Score
Alignment
lac
nan
20.55

                   5.4e-07                 2.4e-07                                                                             
                   *________+1______*      *_____-3__*                                                                         
                   AATTGTGACGTTGTTCAC......GGCACCCCAGG                                                                         
                   +A TGTGA+ T+G TCAC      GGCACCCCAGG                                                                         
         1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCAC           
trn9cat
nan
13.71

                                              4.7e-07                                         9.0e-06                          
                                              *_____+3__*                                     *________+1______*               
                                              CCTGGGGTCCC.....................................AATTGTGACGTTGTTCAC               
                                              CCTGG+GTCCC                                     AA TG GACGTTG+TC                 
         1 CTGTGACGGAAGATCACTTCGCAGAATAAATAAATCCTGGTGTCCCTGTTGATACCGGGAAGCCCTGGGCCAACTTTTGGCGAAAATGAGACGTTGATCGGCACG           
ilv
nan
12.71

               7.1e-06                               1.6e-06                                                                   
               *___+2_*                              *________-1______*                                                        
               CGGCGGGG..............................GTGATCTACGTCACAATT                                                        
               CGGCGGGG                              GTGATC+AC+ C CAATT                                                        
         1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAAAATTTTCCATTGTCTCCCCTGTAAAGCTGT           
ara
nan
9.70

                                                                     6.0e-07                                                   
                                                                     *________-1______*                                        
                                                                     GTGATCTACGTCACAATT                                        
                                                                     +TG +C  CGTCACA TT                                        
         1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTTTGCTATGCCATAGCATTTTTATCCATAAG           
male
nan
9.42

                        1.6e-05                    1.6e-05                                                                     
                        *________+1______*         *___+2_*                                                                    
                        AATTGTGACGTTGTTCAC.........CGGCGGGG                                                                    
                        ++ TGT AC+ +G+TCAC         CGG+GGGG                                                                    
         1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGGTTGCCGTATAAAGAAACTAGAGTCCGTTTA           
malt
nan
9.28

                                                   8.1e-07                                                                     
                                                   *________+1______*                                                          
                                                   AATTGTGACGTTGTTCAC                                                          
                                                   AATTGTGAC+ +GT CA+                                                          
         1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAAAACGTCATCGCTTGCATTAGAAAGGTTTCT           
deop2
nan
8.46

                                                                      1.4e-06                                                  
                                                                      *________+1______*                                       
                                                                      AATTGTGACGTTGTTCAC                                       
                                                                      AATTGTGA GT  +TC +                                       
         1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATCGAAGTGTGTTGCGGAGTAGATGTTAGAATA           
pbr322
nan
7.29

                                                                   3.2e-06                                                     
                                                                   *________-1______*                                          
                                                                   GTGATCTACGTCACAATT                                          
                                                                   GTGA+ TAC+ CACA +T                                          
         1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTC           
uxu1
nan
6.94

                           4.1e-06                                                                                             
                           *________+1______*                                                                                  
                           AATTGTGACGTTGTTCAC                                                                                  
                           + TTGTGA GT GTT AC                                                                                  
         1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAGAACTTATACGCCATCTCATCCGATGCAAGC           
ce1cg
nan
6.58

                                                                           5.2e-06                                             
                                                                           *________-1______*                                  
                                                                           GTGATCTACGTCACAATT                                  
                                                                           +TGATC  + TCACAA++                                  
         1 TAATNTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTTCACAAAAATGGAAGTCCACAGTCTTGACAG           
tnaa
nan
5.90

                                                                                     8.4e-06                                   
                                                                                     *________-1______*                        
                                                                                     GTGATCTACGTCACAATT                        
                                                                                     GTGAT     TCACA TT                        
         1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTGTGATTCGATTCACATTTAAACAATTTCAGA           
gale
nan
5.90

                                                        8.4e-06                                                                
                                                        *________-1______*                                                     
                                                        GTGATCTACGTCACAATT                                                     
                                                        +T  TC A+GTCACA TT                                                     
         1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTGTTATGCTATGGTTATTTCATACCATAAGCC           
cya
nan
5.36

                                                            1.2e-05                                                            
                                                            *________+1______*                                                 
                                                            AATTGTGACGTTGTTCAC                                                 
                                                            A  TGT A +TTG+TCAC                                                 
         1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGACCATTTTTTCGTCGTGAAACTAAAAAAACC           
crp
nan
5.25

                                                                             1.3e-05                                           
                                                                             *________-1______*                                
                                                                             GTGATCTACGTCACAATT                                
                                                                             G  A+  ACGTCACA T+                                
         1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGACGTCACATTACCGTGCAGTACAGTTGATAGC           
ompa
nan
4.74

                                                          1.9e-05                                                              
                                                          *________+1______*                                                   
                                                          AATTGTGACGTTGTTCAC                                                   
                                                          A+   TGACG +GTTCAC                                                   
         1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGTTTTCAACTACGTTGTAGACTTTACATCGCC           
malk
nan
4.74

                                                                       1.9e-05                                                 
                                                                       *________+1______*                                      
                                                                       AATTGTGACGTTGTTCAC                                      
                                                                       ++T GTGA GTTG T  C                                      
         1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCTTGCAAAAATCGTGGCGATTTTATGTGCGCA           
tdc
nan
4.44

                                                                                            2.3e-05                            
                                                                                            *________-1______*                 
                                                                                            GTGATCTACGTCACAATT                 
                                                                                            GTGA    ++ CACA +T                 
         1 GATTTTTATACTTTAACTTGTTGATATTTAAAGGTATTTAATTGTAATAACGATACTCTGGAAAGTATTGAAAGTTAATTTGTGAGTGGTCGCACATATCCTGTT           

MOTIF DIAGRAMS

NameE-value   Motifs
lac nan

+1
-3
trn9cat nan

+3
+1
ilv nan

+2
-1
ara nan

-1
male nan

+1
+2
malt nan

+1
deop2 nan

+1
pbr322 nan

-1
uxu1 nan

+1
ce1cg nan

-1
tnaa nan

-1
gale nan

-1
cya nan

+1
crp nan

-1
ompa nan

+1
malk nan

+1
tdc nan

-1
SCALE
| | | | |
1 12.5 25 37.5 50

EXPLANATION OF OUTPUT

The mhmmscan/MCAST output has up to three sections containing your search results:

All three sections are always present in MCAST output. The second two sections will not be present in mhmmscan output unless the -fancy option was specified.

The results in all three sections are sorted by increasing E-value if possible, or by decreasing match score if E-values could not be computed.

DATABASE SEARCH RESULTS

The "Database Search Results" section consists of lines of the following form:

<ID> <E-value> <Score> <Hits> <Span> <Start> <End> <Length> <Description>

These fields contain, for each match found,

ALIGNMENTS

Each alignment lists the sequence identifier, match E-value and log-odds score along the left. On the right, it shows the alignment of the match with the sequence in groups of four segments. An example segment from an alignment is given below, followed by a description of what each line of the segment means. (The example shows p-value score mode. The row of p-values would be replaced by log-odds scores in log-odds score mode. If '--motif-scoring' is not on, the row of p-values or scores is absent.)

hb_P1_element
1.5e-07
55.02
                             2.4e-04                           2.4e-04            1.3e-04
                             *_____+3__*                       *____-2__*         *___+1_*
                             TTTTTTATGCG.......................TTTTATGACT.........CTAATCCG..................................
                              TTTTTAT+ +                       TTTTAT A T         +TAATC+G
          220 CGGAACATTAAAATGATTTTTATTTCTATGCTAAATCTGTTGTATTTACTTTTATAAATTTAATGTGTTTAATCTGTTCACATTTTTAAATACTTCGTATGCTATCNNNN     329 
      


MOTIF DIAGRAMS

The motif diagrams section shows the matches in schematic format. For each match, in the right two columns, it shows the sequence identifier and the match E-value. On the left, it shows the positions and spacings of the hits making up the match. Hits are labeled with numbers corresponding to the order the motifs were given in the query. A plus or minus sign preceding a hit indicates that the hit occurs on the given (+) or reverse complement (-) of the DNA sequence in the database.


PROGRAM PARAMETERS



Derived parameters for E-value calculations
type of distribution: Exponential
source of distribution: Actual sequence scores
status: Too few (0 < 200) scores from matches with short enough spans to estimate E-values.
number of matches: 17
db length: 1890
average minimum p-value: 0
average motif width: 12.3

Program parameters for mhmmscan
HMM file: mcast_out/crp0.meme.html.mhmm
Sequence file: crp0.fasta
Paths: single
Minimum match score: 2.90716
Partial motif matches are: not allowed
Motif scores are: -log(p_value(log_odds)/p-thresh))
P-value threshold for motif hits: 0.0005
E-value threshold for scores: 10
Background: nrdb
Score matrix for pseudocount frequencies: PAM 1
Beta (weight on pseudocount frequencies): 4.00
Zero spacer emission log-odds: true
Maximum allowed gap: 50
Cost factor for gaps: 1.00
Gap open cost: 0.058
Gap extension cost: 0.058
Fancy output format: true

Actual command line:
mhmmscan --fancy --allow-weak-motifs --p-thresh 0.0005 --max-gap 50 --e-thresh 10.0 --eg-cost 1 --pseudo-weight 4.0 mcast_out/crp0.meme.html.mhmm crp0.fasta

CPU: cantor
Total time 0.01 secs.
Overhead 0.00 secs.
18 sequences
0.2 millisec/seq
1.7 microsec/character

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