mast.farntrans5.oops

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.oops (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    32   QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
	  2    22   CQDEETGGFSDKPGNMVDFYHT

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.46
	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
-------------                      -----------                   -------- ------
RATRABGERB                         Rat rab geranylgeranyl tr...    1.4e-48    331
BET2_YEAST                         YPT1/SEC4 PROTEINS GERANY...    1.1e-47    325
PFTB_RAT                           PROTEIN FARNESYLTRANSFERA...    3.1e-40    437
RAM1_YEAST                         PROTEIN FARNESYLTRANSFERA...    3.9e-40    431
CAL1_YEAST                         RAS PROTEINS GERANYLGERAN...    4.2e-33    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
-------------                      --------  -------------
RATRABGERB                          1.4e-48  126_[1]_16_[1]_16_[1]_15_[2]_40
BET2_YEAST                          1.1e-47  66_[2]_31_[1]_16_[1]_19_[1]_15_
                                             [2]_38
PFTB_RAT                            3.1e-40  133_[1]_19_[1]_16_[1]_17_[1]_
                                             28_[2]_74
RAM1_YEAST                          3.9e-40  291_[1]_19_[2]_67
CAL1_YEAST                          4.2e-33  270_[1]_18_[2]_34

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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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RATRABGERB
  Rat rab geranylgeranyl transferase beta-subunit
  LENGTH = 331  COMBINED P-VALUE = 2.87e-49  E-VALUE =  1.4e-48
  DIAGRAM: 126_[1]_16_[1]_16_[1]_15_[2]_40


                                                        [1]
                                                        2.1e-09
                                                        QQPEGGFNGRPNKLPDVCYSWWVL
                                                        +++++ + +      ++  ++
76   KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV

                             [1]                                             [1]
                             5.2e-06                                         7.6
     GSLPIIGR                QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR                QQP
     ++++++++                + +++++  ++         + + + +++                   +++
151  ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP

                                                 [2]
     e-33                                        3.5e-24
     EGGFNGRPNKLPDVCYSWWVLGSLPIIGR               CQDEETGGFSDKPGNMVDFYHT
     +++++++++++++++++++++++++++++               ++++++++++++++++++++++
226  SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL


BET2_YEAST
  YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
  LENGTH = 325  COMBINED P-VALUE = 2.19e-48  E-VALUE =  1.1e-47
  DIAGRAM: 66_[2]_31_[1]_16_[1]_19_[1]_15_[2]_38

                                                                       [2]
                                                                       1.9e-05
                                                                       CQDEETGGF
                                                                       + + + + +
1    MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF

                                                 [1]
                                                 4.3e-09
     SDKPGNMVDFYHT                               QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIG
     +  +  ++ +  +                               +++++ +++     +++   +  ++ + +++
76   APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG

                      [1]                                                [1]
                      7.8e-08                                            3.5e-34
     R                QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR                   QQPEGGF
                        +++++   ++       ++ +++ +++ ++                   +++++++
151  ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL

                                             [2]
                                             6.0e-22
     NGRPNKLPDVCYSWWVLGSLPIIGR               CQDEETGGFSDKPGNMVDFYHT
     +++++++++++++++++++++++++               ++++++++++++++++++++++
226  NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD


PFTB_RAT
  PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
  LENGTH = 437  COMBINED P-VALUE = 6.27e-41  E-VALUE =  3.1e-40
  DIAGRAM: 133_[1]_19_[1]_16_[1]_17_[1]_28_[2]_74


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

                                       [1]
                                       5.8e-05
     CYSWWVLGSLPIIGR                   QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
       ++   + + +++                     ++++ +       +++  ++  ++ + + +
151  APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT

            [1]                                              [1]
            4.3e-09                                          1.9e-29
            QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR                 QQPEGGFNGRPNKLPDVCY
            +  +++  + +   + + +++  ++ + ++ +                 +++++++++++++++++++
226  AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY

                                              [2]
                                              2.0e-19
     SWWVLGSLPIIGR                            CQDEETGGFSDKPGNMVDFYHT
     ++++++ ++++++                            + +++++++ ++++++++++++
301  SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH


RAM1_YEAST
  PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
  LENGTH = 431  COMBINED P-VALUE = 7.79e-41  E-VALUE =  3.9e-40
  DIAGRAM: 291_[1]_19_[2]_67


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

                                               [2]
                                               1.7e-21
     RPNKLPDVCYSWWVLGSLPIIGR                   CQDEETGGFSDKPGNMVDFYHT
     ++++++++++++++++++++++                    ++++++++++++++++++++++
301  RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE


CAL1_YEAST
  RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
  LENGTH = 376  COMBINED P-VALUE = 8.44e-34  E-VALUE =  4.2e-33
  DIAGRAM: 270_[1]_18_[2]_34


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

                         [2]
                         3.0e-14
     GR                  CQDEETGGFSDKPGNMVDFYHT
     ++                   +++ +++++ +++++++++++
301  TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC

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CPU: rocks-155.sdsc.edu
Time 0.013997 secs.

mast meme.farntrans5.oops