mast.lipocalin.oops

EM算法的改进

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MAST - Motif Alignment and Search Tool
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	MAST version 3.5.1 (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.
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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/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.oops (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    19   PMRNFDIQKFAGTWHEIAK
	  2    20   NNVFWILDTDYKNYLIQYMC

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.24
	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 
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SECTION I: HIGH-SCORING SEQUENCES
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	- 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.
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SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
-------------                      -----------                   -------- ------
ICYA_MANSE                                                        5.3e-31    189
BBP_PIEBR                                                         7.5e-30    173
RETB_BOVIN                                                          5e-26    183
MUP2_MOUSE                                                        2.5e-21    180
LACB_BOVIN                                                        6.5e-21    178

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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 [n]  occurrence of motif `n' with p-value less than 0.0001.
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SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
ICYA_MANSE                          5.3e-31  13_[1]_67_[2]_70
BBP_PIEBR                           7.5e-30  12_[1]_64_[2]_58
RETB_BOVIN                            5e-26  10_[1]_71_[2]_63
MUP2_MOUSE                          2.5e-21  23_[1]_62_[2]_56
LACB_BOVIN                          6.5e-21  21_[1]_64_[2]_54

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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,
	   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).
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ICYA_MANSE
  
  LENGTH = 189  COMBINED P-VALUE = 1.05e-31  E-VALUE =  5.3e-31
  DIAGRAM: 13_[1]_67_[2]_70

                  [1]
                  1.0e-18
                  PMRNFDIQKFAGTWHEIAK
                  +++++++++++++++++++
1    GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNSFVSNGVKEYMEGDLE

                             [2]
                             4.6e-20
                             NNVFWILDTDYKNYLIQYMC
                             + ++++++++++++++++++
76   IAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD


BBP_PIEBR
  
  LENGTH = 173  COMBINED P-VALUE = 1.50e-30  E-VALUE =  7.5e-30
  DIAGRAM: 12_[1]_64_[2]_58

                 [1]
                 6.8e-18
                 PMRNFDIQKFAGTWHEIAK
                 +++++++++++++++++++
1    NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYP

                         [2]
                         1.2e-19
                         NNVFWILDTDYKNYLIQYMC
                         ++++++++++++++++++++
76   VGDSKIGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI


RETB_BOVIN
  
  LENGTH = 183  COMBINED P-VALUE = 9.99e-27  E-VALUE =    5e-26
  DIAGRAM: 10_[1]_71_[2]_63

               [1]
               1.5e-16
               PMRNFDIQKFAGTWHEIAK
               ++++++ ++++++++++++
1    ERDCRVSSFRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVG

                              [2]
                              3.7e-17
                              NNVFWILDTDYKNYLIQYMC
                              + ++++++++++++++++++
76   TFTDTEDPAKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPEVQK


MUP2_MOUSE
  
  LENGTH = 180  COMBINED P-VALUE = 5.04e-22  E-VALUE =  2.5e-21
  DIAGRAM: 23_[1]_62_[2]_56

                            [1]
                            3.2e-14
                            PMRNFDIQKFAGTWHEIAK
                            +++++ +++++++++++++
1    MKMLLLLCLGLTLVCVHAEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGNFRLFLEQIHVLEKSLVLKFH

                                  [2]
                                  1.1e-14
                                  NNVFWILDTDYKNYLIQYMC
                                  +++++++++++++++++++
76   TVRDEECSELSMVADKTEKAGEYSVTYDGFNTFTIPKTDYDNFLMAHLINEKDGETFQLMGLYGREPDLSSDIKE


LACB_BOVIN
  
  LENGTH = 178  COMBINED P-VALUE = 1.29e-21  E-VALUE =  6.5e-21
  DIAGRAM: 21_[1]_64_[2]_54

                          [1]
                          6.2e-15
                          PMRNFDIQKFAGTWHEIAK
                          ++++ ++++++++++++++
1    MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQ

                                  [2]
                                  1.5e-13
                                  NNVFWILDTDYKNYLIQYMC
                                  ++++ +++++++ ++++++
76   KWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE

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CPU: rocks-155.sdsc.edu
Time 0.006998 secs.

mast meme.lipocalin.oops