MEME job 14367 MAST analysis: Dean"s Sequences

[John W. Fondon III (Trey)]

>From: address@hidden
>Date: Tue, 10 Feb 1998 14:03:32 +0100 (MET)
>To: address@hidden
>Subject: MEME job 14367 MAST analysis: Dean"s Sequences
>
>***************************************************************************
>*****
>MAST - Motif Alignment and Search Tool
>***************************************************************************
>*****
>        MAST version 2.0 (Release date: 1996/11/17 00:39:06)
>
>        For further information on how to interpret these results or to get
>        a copy of the MAST software please access http://www.sdsc.edu/MEME.
>***************************************************************************
>*****
>
>
>***************************************************************************
>*****
>REFERENCE
>***************************************************************************
>*****
>        If you use this program in your research, please cite:
>
>        Timothy L. Bailey and Charles Elkan,
>        "Fitting a mixture model by expectation maximization to discover
>        motifs in biopolymers", Proceedings of the Second International
>        Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
>        AAAI Press, Menlo Park, California, 1994.
>***************************************************************************
>*****
>
>
>***************************************************************************
>*****
>DATABASE AND MOTIFS
>***************************************************************************
>*****
>        DATABASE meme.14367.data
>        Last updated on Tue Feb 10 14:02:21 1998
>        Database contains 5 sequences, 748 residues
>
>        MOTIFS meme.14367.results
>        MOTIF WIDTH BEST POSSIBLE MATCH
>        ----- ----- -------------------
>          1     8   EVKCYMAC
>          2     8   CLNETGAT
>          3    11   PEDHCEAAFAY
>***************************************************************************
>*****
>
>
>***************************************************************************
>*****
>EXPLANATION OF RESULTS
>***************************************************************************
>*****
>        SECTION I:   HIGH-SCORING SEQUENCES
>                        - the names of sequences containing occurrences of the
>                          motif(s)
>        SECTION II:  MOTIF DIAGRAMS
>                        - the order and spacing of non-overlapping occurrences
>                          of the motif(s) in each of the high-scoring sequences
>        SECTION III: ANNOTATED SEQUENCES
>                        - the high-scoring sequences annotated with the
>                          positions and strengths of the motif occurrences
>***************************************************************************
>*****
>
>
>***************************************************************************
>*****
>SECTION I: HIGH-SCORING SEQUENCES
>***************************************************************************
>*****
>        - Each of the following 5 sequences has e-value of 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
>-------------            -----------                             --------
>------
>PBP-2                                                             1.7e-18
>150
>PBP-5                                                             2.5e-16
>143
>PBP-1                                                               2e-09
>148
>PBP-3                                                             4.4e-08
>154
>LUSH                                                                0.015
>153
>
>
>***************************************************************************
>*****
>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 the value
>          given below in the legend.
>        - 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.
>
>        LEGEND
>        ----------------------------------------------------------------------
>        -d-   `d' residues separate the end of the preceding motif occurrence
>               and the start of the following motif occurrence
>        [n]   occurrence of motif `n' with p-value less than 0.0001
>***************************************************************************
>*****
>
>SEQUENCE NAME            E-VALUE   MOTIF DIAGRAM
>-------------            --------  -------------
>PBP-2                     1.7e-18  16-[2]-16-[2]-16-[1]-49-[3]-18
>PBP-5                     2.5e-16  37-[2]-16-[1]-49-[3]-14
>PBP-1                       2e-09  41-[2]-17-[1]-52-[1]-14
>PBP-3                     4.4e-08  54-[2]-16-[1]-68
>LUSH                        0.015  71-[1]-74
>
>
>
>***************************************************************************
>*****
>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 four 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).
>***************************************************************************
>*****
>
>
>PBP-2
>
>  LENGTH = 150  COMBINED P-VALUE = 3.35e-19  E-VALUE =  1.7e-18
>  DIAGRAM: 16-[2]-16-[2]-16-[1]-49-[3]-18
>
>                     [2]                     [2]                     [1]
>
>                     7.1e-05                 4.7e-08
>3.4e-07
>                     CLNETGAT                CLNETGAT
>EVKCYMAC
>                     ++  + +                 + ++++++                ++++
>+++
>   1
>MSHLVHLTVLLLVGILCLGATSAKPHEEINRDHLLELANECKAETGATDEDVEQLMSHDLPERHEAKCLRACVMK
>
>                                                   [3]
>
>                                                   5.6e-15
>
>                                                   PEDHCEAAFAY
>
>                                                   +++++++++++
>
>  76
>KLQIMDESGKLNKEHAIELVKVMSKHDAEKEDAPAEVVAKCEAIETPEDHCDAAFAYEECIYEQMREHGLELEEH
>
>
>PBP-5
>
>  LENGTH = 143  COMBINED P-VALUE = 4.95e-17  E-VALUE =  2.5e-16
>  DIAGRAM: 37-[2]-16-[1]-49-[3]-14
>
>                                          [2]                     [1]
>
>                                          2.8e-07                 4.4e-06
>
>                                          CLNETGAT                EVKCYMAC
>
>                                          ++ + +++                  ++ +++
>
>   1
>MQSTPIILVAIVLLGAALVRAFDEKEALAKLMESAESCMPEVGATDADLQEMVKKQPASTYAGKCLRACVMKNIG
>
>                                                [3]
>                                                1.6e-14
>                                                PEDHCEAAFAY
>                                                +++++++++++
>  76 ILDANGKLDTEAGHEKAKQYTGNDPAKLKIALDIGETCAAITVPDDHCEAAEAYGTCFRGEAKKHGLL
>
>
>PBP-1
>
>  LENGTH = 148  COMBINED P-VALUE = 3.97e-10  E-VALUE =    2e-09
>  DIAGRAM: 41-[2]-17-[1]-52-[1]-14
>
>                                              [2]                      [1]
>
>                                              3.6e-08
>4.9e-08
>                                              CLNETGAT
>EVKCYMAC
>                                              ++++++++
>++++++ +
>   1
>MVARHFSFFLALLILYDLIPSNQGVEINPTIIKQVRKLRMRCLNQTGASVDVIDKSVKNRILPTDPEIKCFLYCM
>
>                                                        [1]
>                                                        1.5e-05
>                                                        EVKCYMAC
>                                                         ++++++
>  76 FDMFGLIDSQNIMHLEALLEVLPEEIYKTINGLVSSCGTQKGKDGCDTAYETVKCYIAVNGKFIWEEIIVLLG
>
>
>PBP-3
>
>  LENGTH = 154  COMBINED P-VALUE = 8.73e-09  E-VALUE =  4.4e-08
>  DIAGRAM: 54-[2]-16-[1]-68
>
>                                                           [2]
>
>                                                           4.0e-07
>
>                                                           CLNETGAT
>
>                                                           ++++++ +
>
>   1
>MALNGFGRRVSASVLLIALSLLSGALILPPAAAQRDENYPPPGILKMAKPFHDACVEKTGVTEAAIKEFSDGEIH
>
>        [1]
>
>        2.3e-08
>
>        EVKCYMAC
>
>        ++++++++
>
>  76
>EDEKLKCYMNCFFHEIEVVDDNGDVHLEKLFATVPLSMRDKLMEMSKGCVHPEGDTLCHKAWWFHQCWKKADPKH
>
> 151 YFLP
>
>
>LUSH
>
>  LENGTH = 153  COMBINED P-VALUE = 2.97e-03  E-VALUE =    0.015
>  DIAGRAM: 71-[1]-74
>
>
>[1]
>
>5.2e
>
>EVKC
>
>++ +
>   1
>MKHWKRRSSAVFAIVLQVLVLLLPDPAVAMTMEQFLTSLDMIRSGCAPKFKLKTEDLDRLRVGDFNFPPSQDLMC
>
>
>
>     -06
>
>     YMAC
>
>     ++++
>
>  76
>YTKCVSLMAGTVNKKGEFNAPKALAQLPHLVPPEMMEMSRKSVEACRDTHKQFKESCERVYQTAKCFSENADGQF
>
> 151 MWP
>
>CPU: cleopatre.pasteur.fr
>Time 0.054656 secs.
>
>/local/gensoft/lib/meme/bin/decalpha/mast mast.logodds.14447.tmp
>meme.14367.data ACDEFGHIKLMNPQRSTVWY -nostatus -mf meme.14367.results
>



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