mast.adh.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/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.zoops (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    27   YSASKFAVRMLTRSMRREYAPHGIRVN
	  2    25   QGKVVLITGCSSGIGKATAKHLHKE

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.27
	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
********************************************************************************
	- 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.
********************************************************************************

SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
-------------                      -----------                   -------- ------
YRTP_BACSU                         HYPOTHETICAL 25.3 KD PROT...    5.2e-34    238
BUDC_KLETE                         ACETOIN(DIACETYL) REDUCTA...    7.4e-34    241
AP27_MOUSE                         ADIPOCYTE P27 PROTEIN (AP...    3.7e-28    244
FIXR_BRAJA                         FIXR PROTEIN                     2e-27    278
DHII_HUMAN                         CORTICOSTEROID 11-BETA-DE...    9.7e-27    292
DHGB_BACME                         GLUCOSE 1-DEHYDROGENASE B...      1e-26    262
HDE_CANTR                          HYDRATASE-DEHYDROGENASE-E...    2.2e-26    906
HDHA_ECOLI                         7-ALPHA-HYDROXYSTEROID DE...    2.3e-26    255
NODG_RHIME                         NODULATION PROTEIN G (HOS...    6.1e-26    245
YINL_LISMO                         HYPOTHETICAL 26.8 KD PROT...    1.2e-25    248
RIDH_KLEAE                         RIBITOL 2-DEHYDROGENASE (...    6.7e-25    249
HMTR_LEIMA                         no comment                     7.7e-25    287
FVT1_HUMAN                         no comment                     1.8e-24    332
DHMA_FLAS1                         N-ACYLMANNOSAMINE 1-DEHYD...    4.3e-24    270
DHB2_HUMAN                         no comment                     5.7e-24    387
3BHD_COMTE                         3-BETA-HYDROXYSTEROID DEH...    1.2e-23    253
ENTA_ECOLI                         2,3-DIHYDRO-2,3-DIHYDROXY...    2.4e-23    248
BA72_EUBSP                         7-ALPHA-HYDROXYSTEROID DE...    2.6e-23    249
2BHD_STREX                         20-BETA-HYDROXYSTEROID DE...    3.7e-23    255
BDH_HUMAN                          D-BETA-HYDROXYBUTYRATE DE...    7.5e-23    343
DHES_HUMAN                         ESTRADIOL 17 BETA-DEHYDRO...    3.2e-22    327
GUTD_ECOLI                         SORBITOL-6-PHOSPHATE 2-DE...    5.9e-22    259
DHB3_HUMAN                         no comment                     7.5e-22    310
BPHB_PSEPS                         BIPHENYL-CIS-DIOL DEHYDRO...    5.4e-20    275
LIGD_PSEPA                         C ALPHA-DEHYDROGENASE (EC...    1.1e-19    305
RFBB_NEIGO                         no comment                     1.1e-18    346
DHCA_HUMAN                         no comment                       7e-17    276
MAS1_AGRRA                         no comment                     8.5e-16    476
PCR_PEA                            no comment                     1.3e-15    399
ADH_DROME                          ALCOHOL DEHYDROGENASE (EC...    8.2e-15    255
YURA_MYXXA                         no comment                     2.6e-12    258
FABI_ECOLI                         no comment                       9e-10    262
CSGA_MYXXA                         no comment                       6e-08    166

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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
-------------                      --------  -------------
YRTP_BACSU                          5.2e-34  4_[2]_125_[1]_57
BUDC_KLETE                          7.4e-34  [2]_33_[1]_66_[1]_63
AP27_MOUSE                          3.7e-28  5_[2]_118_[1]_69
FIXR_BRAJA                            2e-27  34_[2]_129_[1]_63
DHII_HUMAN                          9.7e-27  32_[2]_125_[1]_83
DHGB_BACME                            1e-26  5_[2]_129_[1]_76
HDE_CANTR                           2.2e-26  6_[2]_131_[1]_131_[2]_121_[1]_
                                             235_[2]_153
HDHA_ECOLI                          2.3e-26  9_[2]_80_[1]_17_[1]_70
NODG_RHIME                          6.1e-26  4_[2]_122_[1]_67
YINL_LISMO                          1.2e-25  3_[2]_125_[1]_68
RIDH_KLEAE                          6.7e-25  12_[2]_122_[1]_63
HMTR_LEIMA                          7.7e-25  4_[2]_163_[1]_68
FVT1_HUMAN                          1.8e-24  30_[2]_130_[1]_120
DHMA_FLAS1                          4.3e-24  12_[2]_127_[1]_79
DHB2_HUMAN                          5.7e-24  80_[2]_126_[1]_129
3BHD_COMTE                          1.2e-23  4_[2]_30_[1]_64_[1]_76
ENTA_ECOLI                          2.4e-23  3_[2]_115_[1]_78
BA72_EUBSP                          2.6e-23  4_[2]_35_[1]_65_[1]_66
2BHD_STREX                          3.7e-23  4_[2]_122_[1]_77
BDH_HUMAN                           7.5e-23  53_[2]_129_[1]_109
DHES_HUMAN                          3.2e-22  [2]_129_[1]_146
GUTD_ECOLI                          5.9e-22  [2]_128_[1]_79
DHB3_HUMAN                          7.5e-22  46_[2]_126_[1]_86
BPHB_PSEPS                          5.4e-20  3_[2]_124_[1]_96
LIGD_PSEPA                          1.1e-19  4_[2]_127_[1]_122
RFBB_NEIGO                          1.1e-18  4_[2]_135_[1]_155
DHCA_HUMAN                            7e-17  2_[2]_34_[1]_104_[1]_57
MAS1_AGRRA                          8.5e-16  243_[2]_123_[1]_58
PCR_PEA                             1.3e-15  84_[2]_34_[1]_229
ADH_DROME                           8.2e-15  4_[2]_122_[1]_77
YURA_MYXXA                          2.6e-12  159_[1]_72
FABI_ECOLI                            9e-10  4_[2]_129_[1]_77
CSGA_MYXXA                            6e-08  87_[1]_52

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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 = 1.57e-35  E-VALUE =  5.2e-34
  DIAGRAM: 4_[2]_125_[1]_57

         [2]
         2.0e-20
         QGKVVLITGCSSGIGKATAKHLHKE
         +++ +++++++++++++++++++++
1    MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRTSANVEKVAEEVKALGVKAAFAAADVKDADQVNQAVA

         [1]
         2.0e-22
         YSASKFAVRMLTRSMRREYAPHGIRVN
         ++++++++ ++++++++++++++++++
151  VTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASDMSIELNLTDGNPEKVMQPEDLAEYMVAQLKLDPR


BUDC_KLETE
  ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5) (ACETOIN DEHYDROGENASE)
  LENGTH = 241  COMBINED P-VALUE = 2.24e-35  E-VALUE =  7.4e-34
  DIAGRAM: [2]_33_[1]_66_[1]_63

     [2]                                                       [1]
     1.5e-20                                                   7.7e-05
     QGKVVLITGCSSGIGKATAKHLHKE                                 YSASKFAVRMLTRSMRR
     +++++++++++++++++++++++++                                   +    + + ++ +++
1    MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARK

     
     
     EYAPHGIRVN
      ++  ++ ++
76   ALGGFNVIVNNAGIAPSTPIESITEEIVDRVYNINVKGVIWGMQAAVEAFKKEGHGGKIVNACSQAGHVGNPELA

      [1]
      3.9e-22
      YSASKFAVRMLTRSMRREYAPHGIRVN
      +++++++++++++++++++++++++++
151  VYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLK


AP27_MOUSE
  ADIPOCYTE P27 PROTEIN (AP27)
  LENGTH = 244  COMBINED P-VALUE = 1.14e-29  E-VALUE =  3.7e-28
  DIAGRAM: 5_[2]_118_[1]_69

          [2]
          7.6e-16
          QGKVVLITGCSSGIGKATAKHLHKE
          ++  ++++++++++++ ++++++++
1    MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAKECPGIEPVCVDLGDWDATEKALGGIG

                                                                              [1
                                                                              4.
                                                                              YS
                                                                              ++
76   PVDLLVNNAALVIMQPFLEVTKEAFDRSFSVNLRSVFQVSQMVARDMINRGVPGSIVNVSSMVAHVTFPNLITYS

     ]
     3e-21
     ASKFAVRMLTRSMRREYAPHGIRVN
     ++++++++++++++++++++ ++++
151  STKGAMTMLTKAMAMELGPHKIRVNSVNPTVVLTDMGKKVSADPEFARKLKERHPLRKFAEVEDVVNSILFLLSD


FIXR_BRAJA
  FIXR PROTEIN
  LENGTH = 278  COMBINED P-VALUE = 6.20e-29  E-VALUE =    2e-27
  DIAGRAM: 34_[2]_129_[1]_63

                                       [2]
                                       1.7e-16
                                       QGKVVLITGCSSGIGKATAKHLHKE
                                       + ++++ +++++++++++++ + ++
1    MGLDLPNDNLIRGPLPEAHLDRLVDAVNARVDRGEPKVMLLTGASRGIGHATAKLFSEAGWRIISCARQPFDGER

                                           [1]
                                           8.0e-20
                                           YSASKFAVRMLTRSMRREYAPHGIRVN
                                           +  +++++ ++++++++++++++++++
151  APILLAQGLFDELRAASGSIVNVTSIAGSRVHPFAGSAYATSKAALASLTRELAHDYAPHGIRVNAIAPGEIRTD


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 = 2.94e-28  E-VALUE =  9.7e-27
  DIAGRAM: 32_[2]_125_[1]_83

                                     [2]
                                     7.5e-20
                                     QGKVVLITGCSSGIGKATAKHLHKE