mast.farntrans5.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/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.tcm (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    30   GGFQGRPNKEVHTCYTYWALAALAILNKLH
	  2    14   INKEKLIQWIKSCQ

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.22
	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...    2.9e-27    325
RATRABGERB                         Rat rab geranylgeranyl tr...    1.4e-25    331
CAL1_YEAST                         RAS PROTEINS GERANYLGERAN...    9.7e-22    376
PFTB_RAT                           PROTEIN FARNESYLTRANSFERA...    7.6e-21    437
RAM1_YEAST                         PROTEIN FARNESYLTRANSFERA...    6.2e-20    431

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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                          2.9e-27  6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_
                                             3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_
                                             4_[1]_24
RATRABGERB                          1.4e-25  65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_
                                             3_[1]_18_[1]_1_[2]_4_[1]_26
CAL1_YEAST                          9.7e-22  125_[2]_50_[2]_1_[1]_4_[2]_22_
                                             [1]_22_[1]_5_[2]_1
PFTB_RAT                            7.6e-21  120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_
                                             3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60
RAM1_YEAST                          6.2e-20  144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_
                                             1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4

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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 = 5.77e-28  E-VALUE =  2.9e-27
  DIAGRAM: 6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_4_[1]_24

           [2]              [1]                            [2]               [1]
           5.2e-05          2.7e-10                        6.6e-10           5.9
           INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ    GGF
             +++ +++++++     ++  + +++ +++ +++++ +++++++ + ++++++++++++++    + +
1    MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF

                                    [2]              [1]
     e-14                           4.8e-07          2.3e-17
     QGRPNKEVHTCYTYWALAALAILNKLH    INKEKLIQWIKSCQ   GGFQGRPNKEVHTCYTYWALAALAILN
     +  +++++++  +  ++++++ +++++    +++ +++++++ ++   + ++++  +++++++ +++++++++++
76   APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG

         [2]              [1]                                                [1]