MDscan Output

The following is a typical output and explanations:

First the output includes the user-specfied job information as a reminder. It also has the jobID, time submitted, the parameters used in the job, and information on how to generate a sequence logo from reported motifs.

Job information: Test
JobID: 0; Submit date: Fri Apr 23 11:03:02 PDT 2004
Job parameters: Motif width 7; Seed with 10 top sequences; Retain 20 candidate motifs; Report 5 motifs; Background yeast_int.bg;
To generate sequence logo of motifs, paste the aligned sequences below each motif to the following website:
http://weblogo.berkeley.edu/logo.cgi

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*         MDscan Search Result        *
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Based on the probability Pm a pair of characters matching each other, MDscan calculates how many bases of two words needs to match in order to call them similar. In this case, two 8-mers have to match 6 out of the 8 positions in order be considered similar.

Pm 0.2724	Minimum match (6/7)
The highest scoring 5 motifs are:

The program reports the number of top motifs you specified. Each motif looks like the following:

Motif width; score (= log(number of segments) * (relative entropy of the motif) / motif width); Number of aligned sites; consensus and reverse consensus.

Motif 1: Wid 7; Score 4.077; Sites 87; Con TGTTTCA; RCon TGAAACA

The motif matrix in TRANSFAC format, each line represent a motif column. Motif base probability at a column, Consensus (the most abudant base), Reverse (compliment) Consensus, Degenerate (consider all bases with > 25% abudance, represented in IUPAC), Reverse degenerate.

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A      C      G      T       Con  rCon Deg  rDeg
1      1.08  13.92   7.25  77.75      T    A    T    A
2      1.08   0.58  97.25   1.08      G    C    G    C
3      6.64   0.58   0.58  92.19      T    A    T    A
4      1.08   0.58   0.58  97.75      T    A    T    A
5      8.86   3.92   7.25  79.97      T    A    T    A
6      1.08  77.25   6.14  15.53      C    G    C    G
7     85.53   0.58   0.58  13.31      A    T    A    T

Sites contributed to this alignment: sequence name, sequence length, site number (e.g. PRM1/ERG24 contributed 3 sites to the alignment), orientation and location, and sequence of each site. f 326 means 326 from beginning of sequence in forward strand, r 521 means 521 bp from beginning of sequence in reverse strand..

XXX        This site is f 3.
5' ---------- 3'
3' ---------- 5'
XXX       This site is r 4.
>PRM1/ERG24 Len 507	Site #1	f 326
TGTTTCA
>PRM1/ERG24 Len 507	Site #2	f 337
TGTTTCA
>PRM1/ERG24 Len 507	Site #3	f 348
TGTTTCA
>PCL2 Len 1041	Site #1	r 846
TGTTTGA
>PCL2 Len 1041	Site #2	r 521
TGTTTCA
>PCL2 Len 1041	Site #3	f 534
TGTTACA
>PCL2 Len 1041	Site #4	r 438
TGTTTCT
>PCL2 Len 1041	Site #5	f 853
TGTTACA
>FIG2 Len 589	Site #1	r 145
GGTTTCA
>STE12 Len 559	Site #1	f 73
TGTTGCA
>STE12 Len 559	Site #2	r 481
TGTTTGA
>STE12 Len 559	Site #3	f 114
...
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Thanks for using MDscan.