mast.farntrans5.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/farntrans5.s (peptide)
	Last updated on Tue Jan 31 18:16:52 2006
	Database contains 5 sequences, 1900 residues

	MOTIFS /home/meme/TEST/tests/meme.farntrans5.zoops (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    32   QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
	  2    50   GEVDTRFVYCALSVASLLNILTPELVEGAIEFVLRCQNFDGGFGCCPGAE

	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 
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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
-------------                      -----------                   -------- ------
BET2_YEAST                         YPT1/SEC4 PROTEINS GERANY...    2.1e-70    325
RATRABGERB                         Rat rab geranylgeranyl tr...    1.7e-67    331
PFTB_RAT                           PROTEIN FARNESYLTRANSFERA...    9.8e-65    437
RAM1_YEAST                         PROTEIN FARNESYLTRANSFERA...    1.1e-63    431
CAL1_YEAST                         RAS PROTEINS GERANYLGERAN...    7.3e-25    376

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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
-------------                      --------  -------------
BET2_YEAST                          2.1e-70  31_[2]_50_[2]_37_[1]_17_[1]_26
RATRABGERB                          1.7e-67  42_[2]_46_[2]_34_[1]_17_[1]_28
PFTB_RAT                            9.8e-65  133_[1]_31_[2]_35_[1]_30_[1]_62
RAM1_YEAST                          1.1e-63  205_[2]_36_[1]_108
CAL1_YEAST                          7.3e-25  212_[2]_8_[1]_20_[1]_22

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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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BET2_YEAST
  YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
  LENGTH = 325  COMBINED P-VALUE = 4.14e-71  E-VALUE =  2.1e-70
  DIAGRAM: 31_[2]_50_[2]_37_[1]_17_[1]_26

                                    [2]
                                    2.3e-05
                                    GEVDTRFVYCALSVASLLNILTPELVEGAIEFVLRCQNFDGGFG
                                          +++  ++++  +      + + ++ +++++     +
1    MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF

                                                             [2]
                                                             8.6e-45
     CCPGAE                                                  GEVDTRFVYCALSVASLLN
     +                                                       +++++++++ +++++++++
76   APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG

                                                                         [1]
                                                                         3.5e-34
     ILTPELVEGAIEFVLRCQNFDGGFGCCPGAE                                     QQPEGGF
     +++++++ +++++++++++++++++++++++                                     +++++++
151  ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL

                                               [1]
                                               1.0e-06
     NGRPNKLPDVCYSWWVLGSLPIIGR                 QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
     +++++++++++++++++++++++++                     ++   +++  +++  +    + + +++
226  NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD


RATRABGERB
  Rat rab geranylgeranyl transferase beta-subunit
  LENGTH = 331  COMBINED P-VALUE = 3.40e-68  E-VALUE =  1.7e-67
  DIAGRAM: 42_[2]_46_[2]_34_[1]_17_[1]_28

                                               [2]
                                               4.7e-09
                                               GEVDTRFVYCALSVASLLNILTPELVEGAIEFV
                                                     +++  +++  +++ +   + +  + ++
1    MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI

                                                                    [2]
                                                                    3.3e-43
     LRCQNFDGGFGCCPGAE                                              GEVDTRFVYCAL
     ++++   ++  +  +                                                ++++++++++++
76   KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV

                                                                             [1]
                                                                             7.6
     SVASLLNILTPELVEGAIEFVLRCQNFDGGFGCCPGAE                                  QQP
     ++++++++++++++++++++++++++++++++++++++                                  +++
151  ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP

                                                   [1]
     e-33                                          2.1e-07
     EGGFNGRPNKLPDVCYSWWVLGSLPIIGR                 QQPEGGFNGRPNKLPDVCYSWWVLGSLPI
     +++++++++++++++++++++++++++++                   + +++  ++  +++   +    + + +
226  SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL

     
     
     IGR
     ++
301  LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS


PFTB_RAT
  PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
  LENGTH = 437  COMBINED P-VALUE = 1.95e-65  E-VALUE =  9.8e-65
  DIAGRAM: 133_[1]_31_[2]_35_[1]_30_[1]_62


                                                               [1]
                                                               5.4e-09
                                                               QQPEGGFNGRPNKLPDV
                                                               +++++++ + +   +
76   EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL

                                                   [2]
                                                   4.2e-44
     CYSWWVLGSLPIIGR                               GEVDTRFVYCALSVASLLNILTPELVEGA
       ++   + + +++                                +++++++++++++++++++++++++++++
151  APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT

                                                             [1]
                                                             1.9e-29
     IEFVLRCQNFDGGFGCCPGAE                                   QQPEGGFNGRPNKLPDVCY
     +++++++++++++++++++++                                   +++++++++++++++++++
226  AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY

                                                [1]
                                                6.3e-07
     SWWVLGSLPIIGR                              QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
     ++++++ ++++++                              + + +++   + +  +   +  +++ + +
301  SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH


RAM1_YEAST
  PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
  LENGTH = 431  COMBINED P-VALUE = 2.14e-64  E-VALUE =  1.1e-63
  DIAGRAM: 205_[2]_36_[1]_108


                                                            [2]
                                                            3.3e-45
                                                            GEVDTRFVYCALSVASLLNI
                                                            ++++++++++++++++++++
151  PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI

                                                                       [1]
                                                                       2.8e-27
     LTPELVEGAIEFVLRCQNFDGGFGCCPGAE                                    QQPEGGFNG
     +++++++++++++++++++++++++++++                                      ++++++++
226  LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG

     
     
     RPNKLPDVCYSWWVLGSLPIIGR
     ++++++++++++++++++++++
301  RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE


CAL1_YEAST
  RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
  LENGTH = 376  COMBINED P-VALUE = 1.46e-25  E-VALUE =  7.3e-25
  DIAGRAM: 212_[2]_8_[1]_20_[1]_22


                                                                   [2]
                                                                   7.4e-06
                                                                   GEVDTRFVYCALS
                                                                    +       ++++
151  DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS

                                                  [1]
                                                  2.8e-27
     VASLLNILTPELVEGAIEFVLRCQNFDGGFGCCPGAE        QQPEGGFNGRPNKLPDVCYSWWVLGSLPII
     +++++  +         + +           ++   +        ++++++++++++++++++++++++++++++
226  TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL

                           [1]
                           6.4e-05
     GR                    QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
     ++                        +++    +  ++   +    + +++++
301  TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC

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CPU: rocks-155.sdsc.edu
Time 0.030995 secs.

mast meme.farntrans5.zoops