mast.adh.oops

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/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.oops (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    29   YSASKFAVRMLTRSMAHEYAPHGIRVNCI
	  2    29   KVVLITGCSSGIGKATAKHLHKEGAKVVL

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.30
	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 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
-------------                      -----------                   -------- ------
BUDC_KLETE                         ACETOIN(DIACETYL) REDUCTA...    2.6e-33    241
YRTP_BACSU                         HYPOTHETICAL 25.3 KD PROT...    4.3e-33    238
AP27_MOUSE                         ADIPOCYTE P27 PROTEIN (AP...    4.5e-33    244
HDE_CANTR                          HYDRATASE-DEHYDROGENASE-E...    1.6e-32    906
HDHA_ECOLI                         7-ALPHA-HYDROXYSTEROID DE...    4.9e-31    255
DHII_HUMAN                         CORTICOSTEROID 11-BETA-DE...    8.2e-31    292
FIXR_BRAJA                         FIXR PROTEIN                   2.6e-30    278
DHGB_BACME                         GLUCOSE 1-DEHYDROGENASE B...    3.2e-30    262
NODG_RHIME                         NODULATION PROTEIN G (HOS...    3.4e-29    245
RIDH_KLEAE                         RIBITOL 2-DEHYDROGENASE (...    6.2e-29    249
YINL_LISMO                         HYPOTHETICAL 26.8 KD PROT...    6.6e-29    248
DHMA_FLAS1                         N-ACYLMANNOSAMINE 1-DEHYD...    1.2e-28    270
HMTR_LEIMA                         no comment                     5.1e-28    287
2BHD_STREX                         20-BETA-HYDROXYSTEROID DE...    5.9e-28    255
ENTA_ECOLI                         2,3-DIHYDRO-2,3-DIHYDROXY...    4.8e-27    248
DHB2_HUMAN                         no comment                     1.7e-26    387
BDH_HUMAN                          D-BETA-HYDROXYBUTYRATE DE...    2.8e-26    343
BA72_EUBSP                         7-ALPHA-HYDROXYSTEROID DE...    4.2e-26    249
FVT1_HUMAN                         no comment                     8.9e-26    332
GUTD_ECOLI                         SORBITOL-6-PHOSPHATE 2-DE...    5.1e-25    259
DHB3_HUMAN                         no comment                     8.3e-25    310
3BHD_COMTE                         3-BETA-HYDROXYSTEROID DEH...    1.4e-24    253
LIGD_PSEPA                         C ALPHA-DEHYDROGENASE (EC...    8.1e-24    305
DHES_HUMAN                         ESTRADIOL 17 BETA-DEHYDRO...    2.4e-22    327
RFBB_NEIGO                         no comment                     3.2e-19    346
BPHB_PSEPS                         BIPHENYL-CIS-DIOL DEHYDRO...      1e-18    275
YURA_MYXXA                         no comment                     1.9e-18    258
PCR_PEA                            no comment                     7.2e-18    399
DHCA_HUMAN                         no comment                     1.1e-17    276
ADH_DROME                          ALCOHOL DEHYDROGENASE (EC...    2.7e-14    255
MAS1_AGRRA                         no comment                       3e-14    476
FABI_ECOLI                         no comment                     9.7e-14    262
CSGA_MYXXA                         no comment                     2.5e-12    166

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



********************************************************************************
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
-------------                      --------  -------------
BUDC_KLETE                          2.6e-33  2_[2]_120_[1]_61
YRTP_BACSU                          4.3e-33  6_[2]_119_[1]_55
AP27_MOUSE                          4.5e-33  7_[2]_112_[1]_67
HDE_CANTR                           1.6e-32  8_[2]_125_[1]_131_[2]_115_[1]_411
HDHA_ECOLI                          4.9e-31  11_[2]_74_[1]_15_[1]_68
DHII_HUMAN                          8.2e-31  34_[2]_119_[1]_81
FIXR_BRAJA                          2.6e-30  36_[2]_123_[1]_61
DHGB_BACME                          3.2e-30  7_[2]_123_[1]_74
NODG_RHIME                          3.4e-29  6_[2]_116_[1]_65
RIDH_KLEAE                          6.2e-29  14_[2]_116_[1]_61
YINL_LISMO                          6.6e-29  5_[2]_75_[2]_15_[1]_66
DHMA_FLAS1                          1.2e-28  14_[2]_121_[1]_77
HMTR_LEIMA                          5.1e-28  6_[2]_157_[1]_66
2BHD_STREX                          5.9e-28  6_[2]_116_[1]_75
ENTA_ECOLI                          4.8e-27  5_[2]_109_[1]_76
DHB2_HUMAN                          1.7e-26  82_[2]_120_[1]_127
BDH_HUMAN                           2.8e-26  55_[2]_123_[1]_107
BA72_EUBSP                          4.2e-26  6_[2]_121_[1]_64
FVT1_HUMAN                          8.9e-26  32_[2]_124_[1]_118
GUTD_ECOLI                          5.1e-25  2_[2]_122_[1]_77
DHB3_HUMAN                          8.3e-25  48_[2]_120_[1]_84
3BHD_COMTE                          1.4e-24  6_[2]_115_[1]_74
LIGD_PSEPA                          8.1e-24  6_[2]_121_[1]_120
DHES_HUMAN                          2.4e-22  2_[2]_50_[2]_44_[1]_144
RFBB_NEIGO                          3.2e-19  6_[2]_129_[1]_153
BPHB_PSEPS                            1e-18  5_[2]_118_[1]_94
YURA_MYXXA                          1.9e-18  65_[2]_22_[2]_14_[1]_70
PCR_PEA                             7.2e-18  25_[1]_32_[2]_284
DHCA_HUMAN                          1.1e-17  4_[2]_159_[1]_55
ADH_DROME                           2.7e-14  6_[2]_116_[1]_75
MAS1_AGRRA                            3e-14  245_[2]_74_[1]_14_[1]_56
FABI_ECOLI                          9.7e-14  6_[2]_123_[1]_75
CSGA_MYXXA                          2.5e-12  51_[2]_7_[1]_50

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



********************************************************************************
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).
********************************************************************************


BUDC_KLETE
  ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5) (ACETOIN DEHYDROGENASE)
  LENGTH = 241  COMBINED P-VALUE = 7.82e-35  E-VALUE =  2.6e-33
  DIAGRAM: 2_[2]_120_[1]_61

       [2]
       7.9e-21
       KVVLITGCSSGIGKATAKHLHKEGAKVVL
       +++++++++++++++++++++++++ + +
1    MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARK

      [1]
      2.6e-21
      YSASKFAVRMLTRSMAHEYAPHGIRVNCI
      +++++++++++++++++++++ ++++++
151  VYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLK


YRTP_BACSU
  HYPOTHETICAL 25.3 KD PROTEIN IN RTP 5'REGION (ORF238)
  LENGTH = 238  COMBINED P-VALUE = 1.31e-34  E-VALUE =  4.3e-33
  DIAGRAM: 6_[2]_119_[1]_55

           [2]
           2.8e-19
           KVVLITGCSSGIGKATAKHLHKEGAKVVL
           ++++++++++++++++++++++++ ++ +
1    MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRTSANVEKVAEEVKALGVKAAFAAADVKDADQVNQAVA

         [1]
         1.3e-22
         YSASKFAVRMLTRSMAHEYAPHGIRVNCI
         ++++++++ ++++++++++++++++++++
151  VTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASDMSIELNLTDGNPEKVMQPEDLAEYMVAQLKLDPR


AP27_MOUSE
  ADIPOCYTE P27 PROTEIN (AP27)
  LENGTH = 244  COMBINED P-VALUE = 1.37e-34  E-VALUE =  4.5e-33
  DIAGRAM: 7_[2]_112_[1]_67

            [2]
            7.4e-20
            KVVLITGCSSGIGKATAKHLHKEGAKVVL
             +++++++++++++ ++++++++++++++
1    MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAKECPGIEPVCVDLGDWDATEKALGGIG

                                                                              [1
                                                                              4.
                                                                              YS
                                                                              ++
76   PVDLLVNNAALVIMQPFLEVTKEAFDRSFSVNLRSVFQVSQMVARDMINRGVPGSIVNVSSMVAHVTFPNLITYS

     ]
     8e-22
     ASKFAVRMLTRSMAHEYAPHGIRVNCI
     ++++++++++++++++++++ ++++++
151  STKGAMTMLTKAMAMELGPHKIRVNSVNPTVVLTDMGKKVSADPEFARKLKERHPLRKFAEVEDVVNSILFLLSD


HDE_CANTR
  HYDRATASE-DEHYDROGENASE-EPIMERASE (HDE)
  LENGTH = 906  COMBINED P-VALUE = 4.94e-34  E-VALUE =  1.6e-32
  DIAGRAM: 8_[2]_125_[1]_131_[2]_115_[1]_411

             [2]
             2.5e-19
             KVVLITGCSSGIGKATAKHLHKEGAKVVL
             ++++++++++++++ + +++++ ++++++
1    MSPVDFKDKVVIITGAGGGLGKYYSLEFAKLGAKVVVNDLGGALNGQGGNSKAADVVVDEIVKNGGVAVADYNNV

                 [1]
                 2.8e-13
                 YSASKFAVRMLTRSMAHEYAPHGIRVNCI
                 + +++ ++ ++ ++++++ ++++++ +++
151  PAGLYGNFGQANYASAKSALLGFAETLAKEGAKYNIKANAIAPLARSRMTESILPPPMLEKLGPEKVAPLVLYLS

                           [2]
                           1.5e-24
                           KVVLITGCSSGIGKATAKHLHKEGAKVVL
                           +++++++++ +++++++++++++++++++
301  TNEARKLPANDASGAPTVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFKDATKTVDEIKAAGGEAWPDQ

                     [1]
                     5.2e-18
                     YSASKFAVRMLTRSMAHEYAPHGIRVNCI
                     ++++++++ +++++++ + ++ +++++++
451  NITSTSGIYGNFGQANYSSSKAGILGLSKTMAIEGAKNNIKVNIVAPHAETAMTLTIFREQDKNLYHADQVAPLL


HDHA_ECOLI
  7-ALPHA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.159) (HSDH)
  LENGTH = 255  COMBINED P-VALUE = 1.49e-32  E-VALUE =  4.9e-31
  DIAGRAM: 11_[2]_74_[1]_15_[1]_68

                [2]
                4.3e-21