mast.crp0.oops

EM算法的改进

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MAST - Motif Alignment and Search Tool
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	MAST version 3.5.3 (Release date: 2006-03-08 09:30:25 +1000 (Wed, 08 Mar 2006))

	For further information on how to interpret these results or to get
	a copy of the MAST software please access http://meme.nbcr.net.
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REFERENCE
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	If you use this program in your research, please cite:

	Timothy L. Bailey and Michael Gribskov,
	"Combining evidence using p-values: application to sequence homology
	searches", Bioinformatics, 14(48-54), 1998.
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DATABASE AND MOTIFS
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	DATABASE /home/tbailey/meme_trunk/scripts/../tests/crp0.s (nucleotide)
	Last updated on Mon May 29 14:53:46 2006
	Database contains 18 sequences, 1890 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS /home/tbailey/meme_trunk/scripts/../tests/meme.crp0.oops (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    15   GTGACCCGGTTCACA
	  2    15   ACAAAAAACCGTAAA

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.21
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.281 C 0.222 G 0.229 T 0.267 
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SECTION I: HIGH-SCORING SEQUENCES
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	- Each of the following 18 sequences has E-value less than 10.
	- The E-value of a sequence is the expected number of sequences
	  in a random database of the same size that would match the motifs as
	  well as the sequence does and is equal to the combined p-value of the
	  sequence times the number of sequences in the database.
	- The combined p-value of a sequence measures the strength of the
	  match of the sequence to all the motifs and is calculated by
	    o finding the score of the single best match of each motif
	      to the sequence (best matches may overlap),
	    o calculating the sequence p-value of each score,
	    o forming the product of the p-values,
	    o taking the p-value of the product.
	- The sequence p-value of a score is defined as the
	  probability of a random sequence of the same length containing
	  some match with as good or better a score.
	- The score for the match of a position in a sequence to a motif
	  is computed by by summing the appropriate entry from each column of
	  the position-dependent scoring matrix that represents the motif.
	- Sequences shorter than one or more of the motifs are skipped.
	- The table is sorted by increasing E-value.
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SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
-------------                      -----------                   -------- ------
ara                                17 55                          2.8e-06    105
ompa                               48                             8.8e-06    105
ce1cg                              17 61                          0.00025    105
bglr1                              76                              0.0014    105
cya                                50                              0.0031    105
malk                               29 61                            0.004    105
tnaa                               71                              0.0042    105
lac                                9 80                            0.0077    105
deop2                              7 60                             0.013    105
uxu1                               17                               0.013    105
pbr322                             53                               0.015    105
malt                               41                               0.025    105
gale                               42                               0.033    105
crp                                63                               0.055    105
tdc                                78                               0.063    105
ilv                                39                               0.073    105
male                               14                                 0.2    105
trn9cat                            1 84                              0.63    105

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SECTION II: MOTIF DIAGRAMS
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	- The ordering and spacing of all non-overlapping motif occurrences
	  are shown for each high-scoring sequence listed in Section I.
	- A motif occurrence is defined as a position in the sequence whose
	  match to the motif has POSITION p-value less than 0.0001.
	- The POSITION p-value of a match is the probability of
	  a single random subsequence of the length of the motif
	  scoring at least as well as the observed match.
	- For each sequence, all motif occurrences are shown unless there
	  are overlaps.  In that case, a motif occurrence is shown only if its
	  p-value is less than the product of the p-values of the other
	  (lower-numbered) motif occurrences that it overlaps.
	- The table also shows the E-value of each sequence.
	- Spacers and motif occurences are indicated by
	   o -d-    `d' residues separate the end of the preceding motif 
		    occurrence and the start of the following motif occurrence
	   o [sn]  occurrence of motif `n' with p-value less than 0.0001.
		    A minus sign indicates that the occurrence is on the
		    reverse complement strand.
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SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
ara                                 2.8e-06  1_[+2]_41_[-1]_33
ompa                                8.8e-06  4_[+2]_32_[+1]_39
ce1cg                               0.00025  7_[-2]_42_[+1]_26
bglr1                                0.0014  [+2]_63_[-1]_12
cya                                  0.0031  18_[-2]_19_[-1]_38
malk                                  0.004  36_[+2]_13_[+1]_26
tnaa                                 0.0042  74_[+1]_16
lac                                  0.0077  11_[-1]_79
deop2                                 0.013  9_[-1]_81
uxu1                                  0.013  20_[+1]_70
pbr322                                0.015  55_[-1]_35
malt                                  0.025  44_[+1]_46
gale                                  0.033  4_[+2]_35_[+1]_36
crp                                   0.055  65_[-1]_25
tdc                                   0.063  81_[+1]_9
ilv                                   0.073  5_[-2]_85
male                                    0.2  16_[-1]_74
trn9cat                                0.63  105

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SECTION III: ANNOTATED SEQUENCES
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	- The positions and p-values of the non-overlapping motif occurrences
	  are shown above the actual sequence for each of the high-scoring
	  sequences from Section I.
	- A motif occurrence is defined as a position in the sequence whose
	  match to the motif has POSITION p-value less than 0.0001 as 
	  defined in Section II.
	- For each sequence, the first line specifies the name of the sequence.
	- The second (and possibly more) lines give a description of the 
	  sequence.
	- Following the description line(s) is a line giving the length, 
	  combined p-value, and E-value of the sequence as defined in Section I.
	- The next line reproduces the motif diagram from Section II.
	- The entire sequence is printed on the following lines.
	- Motif occurrences are indicated directly above their positions in the
	  sequence on lines showing
	   o the motif number of the occurrence (a minus sign indicates that
	  the occurrence is on the reverse complement strand),
	   o the position p-value of the occurrence,
	   o the best possible match to the motif (or its reverse complement), and
	   o columns whose match to the motif has a positive score (indicated 
	     by a plus sign).
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ara
  17 55
  LENGTH = 105  COMBINED P-VALUE = 1.55e-07  E-VALUE =  2.8e-06
  DIAGRAM: 1_[+2]_41_[-1]_33

      [+2]                                                    [-1]
      6.5e-08                                                 3.6e-06
      ACAAAAAACCGTAAA                                         TGTGAACCGGGTCAC
      +++++++++++++++                                         + ++ ++ +++++++
1    GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACT


ompa
  48
  LENGTH = 105  COMBINED P-VALUE = 4.91e-07  E-VALUE =  8.8e-06
  DIAGRAM: 4_[+2]_32_[+1]_39

         [+2]                                           [+1]
         2.7e-07                                        2.9e-06
         ACAAAAAACCGTAAA                                GTGACCCGGTTCACA
         ++++++++++ ++++                                 +++++ ++++++++
1    GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGT


ce1cg
  17 61
  LENGTH = 105  COMBINED P-VALUE = 1.39e-05  E-VALUE =  0.00025
  DIAGRAM: 7_[-2]_42_[+1]_26

            [-2]                                                     [+1]
            2.1e-06                                                  1.3e-05
            TTTACGGTTTTTTGT                                          GTGACCCGGTT
            + +++++++++++++                                           +++++  +++
1    TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTT

     
     
     CACA
     ++++