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 *************************************** * * * MDscan Search Result * * * ***************************************
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. For questions, please contact Xiaole Shirley Liu at xsliu@jimmy.harvard.edu.