mast.adh.tcm

EM算法的改进

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MAST - Motif Alignment and Search Tool
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	MAST version 3.5.1 (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/adh.s (peptide)
	Last updated on Tue Jan 31 18:16:52 2006
	Database contains 33 sequences, 9996 residues

	MOTIFS /home/meme/TEST/tests/meme.adh.tcm (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    22   YCASKFAVRGFTRSMAMEYAPY
	  2    25   QGKVVLITGCSSGIGKATAKHFHKE

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.34
	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 33 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
-------------                      -----------                   -------- ------
YRTP_BACSU                         HYPOTHETICAL 25.3 KD PROT...    2.3e-30    238
BUDC_KLETE                         ACETOIN(DIACETYL) REDUCTA...    8.5e-29    241
YINL_LISMO                         HYPOTHETICAL 26.8 KD PROT...    1.1e-25    248
DHII_HUMAN                         CORTICOSTEROID 11-BETA-DE...      1e-24    292
FVT1_HUMAN                         no comment                     3.4e-24    332
HDE_CANTR                          HYDRATASE-DEHYDROGENASE-E...    5.8e-24    906
AP27_MOUSE                         ADIPOCYTE P27 PROTEIN (AP...    1.1e-23    244
DHGB_BACME                         GLUCOSE 1-DEHYDROGENASE B...    1.2e-22    262
3BHD_COMTE                         3-BETA-HYDROXYSTEROID DEH...    1.8e-22    253
BPHB_PSEPS                         BIPHENYL-CIS-DIOL DEHYDRO...    1.8e-22    275
FIXR_BRAJA                         FIXR PROTEIN                   1.9e-22    278
DHB3_HUMAN                         no comment                     3.2e-22    310
DHES_HUMAN                         ESTRADIOL 17 BETA-DEHYDRO...    6.8e-22    327
RIDH_KLEAE                         RIBITOL 2-DEHYDROGENASE (...    8.2e-22    249
HDHA_ECOLI                         7-ALPHA-HYDROXYSTEROID DE...    8.5e-22    255
NODG_RHIME                         NODULATION PROTEIN G (HOS...    9.2e-22    245
DHB2_HUMAN                         no comment                     1.6e-21    387
ENTA_ECOLI                         2,3-DIHYDRO-2,3-DIHYDROXY...    4.7e-21    248
DHMA_FLAS1                         N-ACYLMANNOSAMINE 1-DEHYD...    8.9e-21    270
HMTR_LEIMA                         no comment                     1.7e-20    287
BA72_EUBSP                         7-ALPHA-HYDROXYSTEROID DE...    3.3e-20    249
BDH_HUMAN                          D-BETA-HYDROXYBUTYRATE DE...    6.2e-20    343
GUTD_ECOLI                         SORBITOL-6-PHOSPHATE 2-DE...      7e-19    259
2BHD_STREX                         20-BETA-HYDROXYSTEROID DE...    8.4e-19    255
LIGD_PSEPA                         C ALPHA-DEHYDROGENASE (EC...    2.4e-17    305
RFBB_NEIGO                         no comment                     4.3e-17    346
ADH_DROME                          ALCOHOL DEHYDROGENASE (EC...    2.8e-14    255
DHCA_HUMAN                         no comment                     1.1e-13    276
MAS1_AGRRA                         no comment                     3.6e-11    476
PCR_PEA                            no comment                     9.6e-11    399
YURA_MYXXA                         no comment                     1.1e-09    258
CSGA_MYXXA                         no comment                     3.5e-08    166
FABI_ECOLI                         no comment                     6.4e-07    262

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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.
********************************************************************************

SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
YRTP_BACSU                          2.3e-30  4_[2]_125_[1]_62
BUDC_KLETE                          8.5e-29  [2]_126_[1]_68
YINL_LISMO                          1.1e-25  3_[2]_125_[1]_73
DHII_HUMAN                            1e-24  32_[2]_125_[1]_88
FVT1_HUMAN                          3.4e-24  30_[2]_130_[1]_125
HDE_CANTR                           5.8e-24  6_[2]_131_[1]_136_[2]_121_[1]_
                                             240_[2]_153
AP27_MOUSE                          1.1e-23  5_[2]_118_[1]_74
DHGB_BACME                          1.2e-22  5_[2]_129_[1]_81
3BHD_COMTE                          1.8e-22  4_[2]_121_[1]_81
BPHB_PSEPS                          1.8e-22  3_[2]_124_[1]_101
FIXR_BRAJA                          1.9e-22  34_[2]_129_[1]_68
DHB3_HUMAN                          3.2e-22  46_[2]_126_[1]_91
DHES_HUMAN                          6.8e-22  [2]_129_[1]_151
RIDH_KLEAE                          8.2e-22  12_[2]_122_[1]_68
HDHA_ECOLI                          8.5e-22  9_[2]_124_[1]_75
NODG_RHIME                          9.2e-22  4_[2]_122_[1]_72
DHB2_HUMAN                          1.6e-21  80_[2]_126_[1]_134
ENTA_ECOLI                          4.7e-21  3_[2]_115_[1]_83
DHMA_FLAS1                          8.9e-21  12_[2]_127_[1]_84
HMTR_LEIMA                          1.7e-20  4_[2]_163_[1]_73
BA72_EUBSP                          3.3e-20  4_[2]_127_[1]_71
BDH_HUMAN                           6.2e-20  53_[2]_129_[1]_114
GUTD_ECOLI                            7e-19  [2]_128_[1]_84
2BHD_STREX                          8.4e-19  4_[2]_122_[1]_82
LIGD_PSEPA                          2.4e-17  4_[2]_127_[1]_127
RFBB_NEIGO                          4.3e-17  4_[2]_135_[1]_160
ADH_DROME                           2.8e-14  4_[2]_122_[1]_82
DHCA_HUMAN                          1.1e-13  2_[2]_165_[1]_62
MAS1_AGRRA                          3.6e-11  243_[2]_123_[1]_63
PCR_PEA                             9.6e-11  84_[2]_290
YURA_MYXXA                          1.1e-09  159_[1]_77
CSGA_MYXXA                          3.5e-08  87_[1]_57
FABI_ECOLI                          6.4e-07  4_[2]_129_[1]_82

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********************************************************************************
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).
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YRTP_BACSU
  HYPOTHETICAL 25.3 KD PROTEIN IN RTP 5'REGION (ORF238)
  LENGTH = 238  COMBINED P-VALUE = 6.86e-32  E-VALUE =  2.3e-30
  DIAGRAM: 4_[2]_125_[1]_62

         [2]
         2.9e-20
         QGKVVLITGCSSGIGKATAKHFHKE
         +++ +++++++++++++++++++++
1    MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRTSANVEKVAEEVKALGVKAAFAAADVKDADQVNQAVA

         [1]
         6.6e-19
         YCASKFAVRGFTRSMAMEYAPY
         ++++++++ +++++++++++++
151  VTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASDMSIELNLTDGNPEKVMQPEDLAEYMVAQLKLDPR


BUDC_KLETE
  ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5) (ACETOIN DEHYDROGENASE)
  LENGTH = 241  COMBINED P-VALUE = 2.57e-30  E-VALUE =  8.5e-29
  DIAGRAM: [2]_126_[1]_68

     [2]
     1.6e-20
     QGKVVLITGCSSGIGKATAKHFHKE
     +++++++++++++++++++++++++
1    MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARK

      [1]
      4.7e-17
      YCASKFAVRGFTRSMAMEYAPY
      +++++++++++++++++++++
151  VYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLK


YINL_LISMO
  HYPOTHETICAL 26.8 KD PROTEIN IN INLA 5'REGION (ORFA)
  LENGTH = 248  COMBINED P-VALUE = 3.19e-27  E-VALUE =  1.1e-25
  DIAGRAM: 3_[2]_125_[1]_73

        [2]
        2.9e-20
        QGKVVLITGCSSGIGKATAKHFHKE
        ++++++++++++++++++++ ++++
1    MTIKNKVIIITGASSGIGKATALLLAEKGAKLVLAARRVEKLEKIVQIIKANSGEAIFAKTDVTKREDNKKLVEL

        [1]
        3.3e-14
        YCASKFAVRGFTRSMAMEYAPY
        +++++++++ +++ ++++ +++
151  GAVYGATKWAVRDLMEVLRMESAQEGTNIRTATIYPAAINTELLETITDKETEQGMTSLYKQYGITPDRIASIVA


DHII_HUMAN
  CORTICOSTEROID 11-BETA-DEHYDROGENASE (EC 1.1.1.146) (11-DH) (11-BETA- 
  HYDROXYSTEROID DEHYDROGENASE) (11-BETA-HSD)
  LENGTH = 292  COMBINED P-VALUE = 3.04e-26  E-VALUE =    1e-24
  DIAGRAM: 32_[2]_125_[1]_88

                                     [2]
                                     1.1e-19
                                     QGKVVLITGCSSGIGKATAKHFHKE
                                     +++ +++++++++++++++++++++
1    MAFMKKYLLPILGLFMAYYYYSANEEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQKVV

                                     [1]
                                     6.1e-14
                                     YCASKFAVRGFTRSMAMEYAPY
                                     +++++++++++ ++ +++++ +
151  TVAALPMLKQSNGSIVVVSSLAGKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTETAMK


FVT1_HUMAN
  no comment
  LENGTH = 332  COMBINED P-VALUE = 1.03e-25  E-VALUE =  3.4e-24
  DIAGRAM: 30_[2]_130_[1]_125

                                   [2]
                                   7.5e-16
                                   QGKVVLITGCSSGIGKATAKHFHKE