mast.lipocalin.tcm

EM算法的改进

********************************************************************************
MAST - Motif Alignment and Search Tool
********************************************************************************
	MAST version 3.5.1 (Release date: 2006/02/01 02:08:55)

	For further information on how to interpret these results or to get
	a copy of the MAST software please access http://meme.nbcr.net.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
	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.
********************************************************************************


********************************************************************************
DATABASE AND MOTIFS
********************************************************************************
	DATABASE /home/meme/TEST/tests/lipocalin.s (peptide)
	Last updated on Tue Jan 31 18:16:52 2006
	Database contains 5 sequences, 903 residues

	MOTIFS /home/meme/TEST/tests/meme.lipocalin.tcm (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    28   HDGRCPDVKPVDNFDWSRFAGTWWEIAK
	  2    42   VFWVLATDNKNYIIGYNCDYDPDKKGHQDHVWILSRSKVLEG

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.23
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
	L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
	W 0.013 Y 0.033 
********************************************************************************


********************************************************************************
SECTION I: HIGH-SCORING SEQUENCES
********************************************************************************
	- Each of the following 5 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.
********************************************************************************

SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
-------------                      -----------                   -------- ------
BBP_PIEBR                                                         4.6e-73    173
ICYA_MANSE                                                        1.4e-70    189
RETB_BOVIN                                                        3.8e-18    183
LACB_BOVIN                                                          0.037    178
MUP2_MOUSE                                                            0.3    180

********************************************************************************



********************************************************************************
SECTION II: MOTIF DIAGRAMS
********************************************************************************
	- 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 [n]  occurrence of motif `n' with p-value less than 0.0001.
********************************************************************************

SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
BBP_PIEBR                           4.6e-73  3_[1]_66_[2]_34
ICYA_MANSE                          1.4e-70  4_[1]_69_[2]_46
RETB_BOVIN                          3.8e-18  1_[1]_154
LACB_BOVIN                            0.037  12_[1]_138
MUP2_MOUSE                              0.3  180

********************************************************************************



********************************************************************************
SECTION III: ANNOTATED SEQUENCES
********************************************************************************
	- 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,
	   o the position p-value of the occurrence,
	   o the best possible match to the motif, and
	   o columns whose match to the motif has a positive score (indicated 
	     by a plus sign).
********************************************************************************


BBP_PIEBR
  
  LENGTH = 173  COMBINED P-VALUE = 9.18e-74  E-VALUE =  4.6e-73
  DIAGRAM: 3_[1]_66_[2]_34

        [1]
        1.9e-32
        HDGRCPDVKPVDNFDWSRFAGTWWEIAK
        ++++++++++++++++++++++++++++
1    NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYP

                           [2]
                           1.4e-48
                           VFWVLATDNKNYIIGYNCDYDPDKKGHQDHVWILSRSKVLEG
                           ++++++++++++++++++++++++++++++++++++++++++
76   VGDSKIGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI


ICYA_MANSE
  
  LENGTH = 189  COMBINED P-VALUE = 2.81e-71  E-VALUE =  1.4e-70
  DIAGRAM: 4_[1]_69_[2]_46

         [1]
         2.6e-29
         HDGRCPDVKPVDNFDWSRFAGTWWEIAK
         ++++++++++++++++++++++++++++
1    GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNSFVSNGVKEYMEGDLE

                               [2]
                               2.6e-49
                               VFWVLATDNKNYIIGYNCDYDPDKKGHQDHVWILSRSKVLEG
                               ++++++++++++++++++++++++++++++++++++++++++
76   IAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD


RETB_BOVIN
  
  LENGTH = 183  COMBINED P-VALUE = 7.60e-19  E-VALUE =  3.8e-18
  DIAGRAM: 1_[1]_154

      [1]
      8.9e-22
      HDGRCPDVKPVDNFDWSRFAGTWWEIAK
      ++++ +++++++++++++++++++++++
1    ERDCRVSSFRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVG


LACB_BOVIN
  
  LENGTH = 178  COMBINED P-VALUE = 7.40e-03  E-VALUE =    0.037
  DIAGRAM: 12_[1]_138

                 [1]
                 5.0e-05
                 HDGRCPDVKPVDNFDWSRFAGTWWEIAK
                    +          +    +++++  +
1    MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQ


MUP2_MOUSE
  
  LENGTH = 180  COMBINED P-VALUE = 6.09e-02  E-VALUE =      0.3
  DIAGRAM: 180


********************************************************************************


CPU: rocks-155.sdsc.edu
Time 0.020996 secs.

mast meme.lipocalin.tcm