mast.crp0.tcm

EM算法的改进

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MAST - Motif Alignment and Search Tool
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	MAST version 3.5.4 (Release date: 3.5.4)

	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 /mnt/hgfs/linuxshare/meme_3.5.4/scripts/../tests/crp0.s (nucleotide)
	Last updated on Fri Sep 22 03:39:19 2006
	Database contains 18 sequences, 1890 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS /mnt/hgfs/linuxshare/meme_3.5.4/scripts/../tests/meme.crp0.tcm (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    19   TGTGAGCGAGGTCACACTT
	  2    11   GTGGAATTGTT

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.28
	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
-------------                      -----------                   -------- ------
gale                               42                             1.3e-05    105
lac                                9 80                           5.9e-05    105
tnaa                               71                             0.00021    105
malt                               41                             0.00027    105
ara                                17 55                          0.00038    105
ce1cg                              17 61                           0.0018    105
uxu1                               17                              0.0045    105
deop2                              7 60                             0.015    105
ompa                               48                               0.017    105
cya                                50                               0.017    105
tdc                                78                               0.026    105
male                               14                               0.027    105
bglr1                              76                               0.032    105
crp                                63                               0.045    105
pbr322                             53                               0.097    105
malk                               29 61                             0.12    105
ilv                                39                                0.22    105
trn9cat                            1 84                                 5    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
-------------                      --------  -------------
gale                                1.3e-05  30_[-2]_3_[+1]_42
lac                                 5.9e-05  11_[+1]_46_[+2]_7_[-2]
tnaa                                0.00021  73_[+1]_1_[-2]_1
malt                                0.00027  40_[-1]_46
ara                                 0.00038  57_[+1]_29
ce1cg                                0.0018  16_[-1]_28_[+1]_23
uxu1                                 0.0045  9_[+2]_85
deop2                                 0.015  9_[+1]_31_[-1]_27
ompa                                  0.017  50_[+1]_36
cya                                   0.017  49_[-1]_37
tdc                                   0.026  78_[+1]_8
male                                  0.027  16_[+1]_70
bglr1                                 0.032  78_[+1]_8
crp                                   0.045  65_[+1]_21
pbr322                                0.097  52_[-1]_34
malk                                   0.12  60_[-1]_26
ilv                                    0.22  41_[+1]_45
trn9cat                                   5  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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gale
  42
  LENGTH = 105  COMBINED P-VALUE = 6.98e-07  E-VALUE =  1.3e-05
  DIAGRAM: 30_[-2]_3_[+1]_42

                                   [-2]          [+1]
                                   1.8e-06       6.6e-07
                                   AACAATTCCAC   TGTGAGCGAGGTCACACTT
                                   +++++++++++   +++  ++++++++++++++
1    GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTG


lac
  9 80
  LENGTH = 105  COMBINED P-VALUE = 3.29e-06  E-VALUE =  5.9e-05
  DIAGRAM: 11_[+1]_46_[+2]_7_[-2]

                [+1]
                9.2e-06
                TGTGAGCGAGGTCACACTT
                ++++++  ++ ++++ +++
1    AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG

      [+2]              [-2]
      1.8e-06           6.6e-07
      GTGGAATTGTT       AACAATTCCAC
      +++++++++++       +++++++++++
76   TGTGGAATTGTGAGCGGATAACAATTTCAC


tnaa
  71 
  LENGTH = 105  COMBINED P-VALUE = 1.19e-05  E-VALUE =  0.00021
  DIAGRAM: 73_[+1]_1_[-2]_1

                                                                              [+
                                                                              1.
                                                                              TG
                                                                              ++
1    TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTG

     1]                [-2]
     0e-05             2.4e-06
     TGAGCGAGGTCACACTT AACAATTCCAC
     ++++ +   +++++ ++ +++++++++++