mast.ino_up800.zoops

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/INO_up800.s (nucleotide)
	Last updated on Tue Jan 31 18:16:52 2006
	Database contains 7 sequences, 5600 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS /home/meme/TEST/tests/meme.INO_up800.zoops (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    16   ACTTTTCACATGCCCC
	  2    21   CACGGCCCCATCACCACTGTC

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.25
	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 7 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
-------------                      -----------                   -------- ------
INO1                               sequence of the region up...    7.6e-10    800
FAS2                               sequence of the region up...    1.6e-08    800
ACC1                               sequence of the region up...    2.7e-07    800
OPI3                               sequence of the region up...    4.6e-07    800
FAS1                               sequence of the region up...    2.4e-06    800
CHO1                               sequence of the region up...    3.2e-06    800
CHO2                               sequence of the region up...     0.0012    800

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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
-------------                      --------  -------------
INO1                                7.6e-10  368_[-2]_181_[-1]_33_[-1]_165
FAS2                                1.6e-08  562_[+1]_131_[+2]_70
ACC1                                2.7e-07  78_[+1]_40_[+2]_645
OPI3                                4.6e-07  503_[-2]_60_[-1]_200
FAS1                                2.4e-06  44_[+2]_25_[+1]_694
CHO1                                3.2e-06  614_[+2]_[+1]_149
CHO2                                 0.0012  349_[+1]_435

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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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INO1
  sequence of the region upstream from YJL153C
  LENGTH = 800  COMBINED P-VALUE = 1.09e-10  E-VALUE =  7.6e-10
  DIAGRAM: 368_[-2]_181_[-1]_33_[-1]_165


                                                                         [-2]
                                                                         4.4e-09
                                                                         GACAGTG
                                                                         + + +++
301  GTGACCTGGAAGCTCACCCTGCAGAGGAATCTCAAGCACAGCCTCCAGCATATGATGAAGACGATGAGGCCGGTG

     
     
     GTGATGGGGCCGTG
      +++++++++++++
376  CCGATGTGCCCTTGATGGACAACAAACAACAGCTCTCTTCCGGCCGTACTTAGTGATCGGAACGAGCTCTTTATC

                                                  [-1]
                                                  9.0e-05
                                                  GGGGCATGTGAAAAGT
                                                  +  + ++++++++  +
526  TGAAATACGTGCCGGTGTTCCGGGGTTGGATGCGGAATCGAAAGTGTTGAATGTGAAATATGCGGAGGCCAAGTA

                        [-1]
                        3.7e-10
                        GGGGCATGTGAAAAGT
                        ++++++++++++++++
601  TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG


FAS2
  sequence of the region upstream from YPL231W
  LENGTH = 800  COMBINED P-VALUE = 2.30e-09  E-VALUE =  1.6e-08
  DIAGRAM: 562_[+1]_131_[+2]_70


                                          [+1]
                                          2.4e-07
                                          ACTTTTCACATGCCCC
                                           ++++++++++++  +
526  GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCATTCGCCTCGTAACGTTAC

                                       [+2]
                                       1.6e-10
                                       CACGGCCCCATCACCACTGTC
                                       ++++ ++++++++++++++++
676  TGCCTCATATATAACTTGTTAACTGAAGGTTACACAAGACCACATCACCACTGTCGTGCTTTTCTAATAACCGCT


ACC1
  sequence of the region upstream from YNR016C
  LENGTH = 800  COMBINED P-VALUE = 3.89e-08  E-VALUE =  2.7e-07
  DIAGRAM: 78_[+1]_40_[+2]_645


        [+1]                                                    [+2]
        1.7e-08                                                 4.4e-08
        ACTTTTCACATGCCCC                                        CACGGCCCCATCACCA
        + ++++++++++++++                                        +++ +++ +++ ++++
76   TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAATTCAACCGCTCATTGCCA

     
     
     CTGTC
     +++++
151  CTCTCTCTACTGCTTGGTGAACTAGGCTATACGCTCAATCAGCGCCAAGATATATAAGAAGAACAGCACTCCCAG


OPI3
  sequence of the region upstream from YJR073C
  LENGTH = 800  COMBINED P-VALUE = 6.52e-08  E-VALUE =  4.6e-07
  DIAGRAM: 503_[-2]_60_[-1]_200


                                                          [-2]
                                                          7.3e-09
                                                          GACAGTGGTGATGGGGCCGTG
                                                          ++++++++++++++ ++++
451  TGTGTATCGGGGACTTCTCTTAGAGTAGAAGCGTCTATAAACCCAGGTGGGACGACAGTAGTGATGGCGCCGCCG

                                                                [-1]
                                                                1.8e-07
                                                                GGGGCATGTGAAAAGT
                                                                 + +++++++ +++++
526  TATAATTCGACTTCCTTGTTGTTCATGCTTCCTTGATGACCAGGGTAGGTGTCAATGAGAGTGCATGTGGAAAGT


FAS1
  sequence of the region upstream from YKL182W
  LENGTH = 800  COMBINED P-VALUE = 3.44e-07  E-VALUE =  2.4e-06
  DIAGRAM: 44_[+2]_25_[+1]_694

                                                 [+2]
                                                 1.9e-07
                                                 CACGGCCCCATCACCACTGTC
                                                 ++ ++ +   +++++++++ +
1    CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCACTACTCCCCTGGCCTCCA

                    [+1]
                    3.9e-08
                    ACTTTTCACATGCCCC
                    +  +++++++++++++
76   ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCGATCTTTCCGTCGCACAA


CHO1
  sequence of the region upstream from YER026C
  LENGTH = 800  COMBINED P-VALUE = 4.51e-07  E-VALUE =  3.2e-06
  DIAGRAM: 614_[+2]_[+1]_149


                   [+2]                 [+1]
                   1.4e-07              6.9e-08
                   CACGGCCCCATCACCACTGTCACTTTTCACATGCCCC
                   ++++++ ++ ++++  ++ + ++ ++++++++++ ++
601  ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAAAGATGAAGATCCGTATT


CHO2
  sequence of the region upstream from YGR157W
  LENGTH = 800  COMBINED P-VALUE = 1.68e-04  E-VALUE =   0.0012
  DIAGRAM: 349_[+1]_435


                                                      [+1]
                                                      8.9e-09
                                                      ACTTTTCACATGCCCC
                                                      +++++++ ++++++++
301  ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTCATGCCGCATTCATTATT

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CPU: rocks-155.sdsc.edu
Time 0.011998 secs.

mast meme.INO_up800.zoops