mhmmscan

DATABASE SEARCH RESULTS

ALIGNMENTS

MOTIF DIAGRAMS

EXPLANATION OF OUTPUT

PROGRAM PARAMETERS

The MEME Suite of motif-based sequence analysis tools.

version 4.4.0 (Release date: 7 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 Apr 20 15:32:10 2010

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

ID	E-value	Score	Hits	Span	Start	End	Description
lac	nan	21.23	2	35	9	43
trn9cat	nan	15.68	2	66	36	101
ilv	nan	13.86	2	56	5	60
male	nan	10.26	2	35	14	48
ara	nan	10.09	1	18	59	76
malt	nan	9.08	1	18	41	58
deop2	nan	8.23	1	18	60	77
ce1cg	nan	7.94	2	66	17	82
pbr322	nan	7.27	1	18	57	74
uxu1	nan	6.93	1	18	17	34
gale	nan	6.29	1	18	46	63
tnaa	nan	5.83	1	18	75	92
cya	nan	5.40	1	18	50	67
crp	nan	5.38	1	18	67	84
malk	nan	4.97	1	18	61	78
ompa	nan	4.76	1	18	48	65
tdc	nan	4.63	1	18	82	99

ALIGNMENTS

ID E-value Score	Alignment
lac nan 21.23	4.0e-07 2.4e-07 ________+1______ _____-3__ AATTGTGACGTTGTTCAC......GGCACCCCAGG +A TGTGA+ T+G TCAC GGCACCCCAGG 1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCAC
trn9cat nan 15.68	4.7e-07 6.8e-06 _____+3__ ________+1______ CCTGGGGTCCC.....................................AATTGTGACGTTGTTCAC CCTGG+GTCCC AA TG GACGTTG+TC 1 CTGTGACGGAAGATCACTTCGCAGAATAAATAAATCCTGGTGTCCCTGTTGATACCGGGAAGCCCTGGGCCAACTTTTGGCGAAAATGAGACGTTGATCGGCACG
ilv nan 13.86	7.1e-06 1.7e-06 ___+2_ ________-1______ CGGCGGGG..............................GTGATCTACGTCACAATT CGGCGGGG GTGATC+AC+ C CAATT 1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAAAATTTTCCATTGTCTCCCCTGTAAAGCTGT
male nan 10.26	1.2e-05 1.6e-05 ________+1______ ___+2_ AATTGTGACGTTGTTCAC.........CGGCGGGG ++ TGT AC+ +G+TCAC CGG+GGGG 1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGGTTGCCGTATAAAGAAACTAGAGTCCGTTTA
ara nan 10.09	4.6e-07 ________-1______ GTGATCTACGTCACAATT +TG +C CGTCACA TT 1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTTTGCTATGCCATAGCATTTTTATCCATAAG
malt nan 9.08	9.2e-07 ________+1______ AATTGTGACGTTGTTCAC AATTGTGAC+ +GT CA+ 1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAAAACGTCATCGCTTGCATTAGAAAGGTTTCT
deop2 nan 8.23	1.7e-06 ________+1______ AATTGTGACGTTGTTCAC AATTGTGA GT +TC + 1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATCGAAGTGTGTTGCGGAGTAGATGTTAGAATA
ce1cg nan 7.94	1.6e-04 4.6e-06 ________+1______ ________-1______ AATTGTGACGTTGTTCAC..............................GTGATCTACGTCACAATT ++TTGTG C+T G C + +TGATC + TCACAA++ 1 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTTCACAAAAATGGAAGTCCACAGTCTTGACAG
pbr322 nan 7.27	3.2e-06 ________-1______ GTGATCTACGTCACAATT GTGA+ TAC+ CACA +T 1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTC
uxu1 nan 6.93	4.1e-06 ________+1______ AATTGTGACGTTGTTCAC + TTGTGA GT GTT AC 1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAGAACTTATACGCCATCTCATCCGATGCAAGC
gale nan 6.29	6.4e-06 ________-1______ GTGATCTACGTCACAATT +T TC A+GTCACA TT 1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTGTTATGCTATGGTTATTTCATACCATAAGCC
tnaa nan 5.83	8.8e-06 ________-1______ GTGATCTACGTCACAATT GTGAT TCACA TT 1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTGTGATTCGATTCACATTTAAACAATTTCAGA
cya nan 5.40	1.2e-05 ________+1______ AATTGTGACGTTGTTCAC A TGT A +TTG+TCAC 1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGACCATTTTTTCGTCGTGAAACTAAAAAAACC
crp nan 5.38	1.2e-05 ________-1______ GTGATCTACGTCACAATT G A+ ACGTCACA T+ 1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGACGTCACATTACCGTGCAGTACAGTTGATAGC
malk nan 4.97	1.6e-05 ________+1______ AATTGTGACGTTGTTCAC ++T GTGA GTTG T C 1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCTTGCAAAAATCGTGGCGATTTTATGTGCGCA
ompa nan 4.76	1.9e-05 ________+1______ AATTGTGACGTTGTTCAC A+ TGACG +GTTCAC 1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGTTTTCAACTACGTTGTAGACTTTACATCGCC
tdc nan 4.63	2.0e-05 ________-1______ GTGATCTACGTCACAATT GTGA ++ CACA +T 1 GATTTTTATACTTTAACTTGTTGATATTTAAAGGTATTTAATTGTAATAACGATACTCTGGAAAGTATTGAAAGTTAATTTGTGAGTGGTCGCACATATCCTGTT

MOTIF DIAGRAMS

Name

E-value

Motifs

lac

nan

-3

trn9cat

nan

ilv

nan

-1

male

nan

ara

nan

-1

malt

nan

deop2

nan

ce1cg

nan

-1

pbr322

nan

-1

uxu1

nan

gale

nan

-1

tnaa

nan

-1

cya

nan

crp

nan

-1

malk

nan

ompa

nan

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:

Database Search Results
Alignments
Motif Diagrams

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,

ID - The sequence identifier, as given in the database file.
E-value - The E-value, which is the total number of matches that you would expect with match scores as good as this match if the database contained only sequences unrelated to the query. Thus, a small E-value indicates a good match.
Score - The match score, which is the sum of the scores for hits, minus the penalties for gaps.
Hits - The number of hits in the match.
Span - The length of the match, measured from the start of the first hit to the end of the last hit.
Start - The position in the sequence where the match begins.
End - The position in the sequence where the match ends.
Length - The length of the sequence that contains the match.
Description - The sequence descriptor. This description is taken from the FASTA database file, and is truncated so that the output fits easily on one line.

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

The bottom-most line in each segment contains 50 letters from the target database sequence, flanked by that segment's start and end locations within the entire sequence. Thus, the first segment would be flanked by "1" and "49", the second by "50" and "99", etc.
Aligned above these 50-letter segments are the motifs corresponding to the hits in the match. The motifs are labeled with numbers in the order they appear 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. Each position within a motif region is indicated by a letter, and each gap position is indicated with a period.
In between the sequence segment and the corresponding match positions is a line that indicates the degree of match between the motifs and the sequence. If the letter in the motif with the largest log-odds score appears in the sequence, then the match row contains that letter. If the sequence letter does not have the largest log-odds score, but does have a positive log-odds score, then the match row contains a plus sign. Otherwise, the match row is empty.
The top-most row of each segment shows the p-value (or log-odds score) of each hit aligned above the start of the hit, depending on the score mode.

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: 3.43e-08
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: 3.1943
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: 100
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: 200
Cost factor for gaps: 1.00
Gap open cost: 0.016
Gap extension cost: 0.016
Fancy output format: true

Actual command line:
mhmmscan --fancy --allow-weak-motifs --p-thresh 0.0005 --max-gap 200 --e-thresh 100.0 --eg-cost 1 --pseudo-weight 4.0 mcast_out/crp0.meme.html.mhmm crp0.fasta

CPU: threonine.gs.washington.edu
Total time 0.01 secs.
Overhead 0.01 secs.
18 sequences
0.2 millisec/seq
1.6 microsec/character

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