MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2004/07/16 05:53:30)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
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/meme.3.0.6/tests/lipocalin.s (peptide)
Last updated on Fri Jul 16 15:53:57 2004
Database contains 5 sequences, 903 residues
MOTIFS meme.lipocalin.tcm.4.Linuxx86_64.html (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 28 HDGRCPDVKPVDNFDWSRFAGTWWEIAK
2 42 VFWVLATDNKNYIIGYNCDYDPDKKGHQDHVWILSRSKVLEG
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.23
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 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
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- 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.
Links | Sequence Name | Description | E-value | Length
|
---|
| BBP_PIEBR
|
| 4.6e-73
| 173
|
| ICYA_MANSE
|
| 1.4e-70
| 189
|
| RETB_BOVIN
|
| 3.8e-18
| 183
|
| LACB_BOVIN
|
| 0.037
| 178
|
| MUP2_MOUSE
|
| 0.3
| 180
|
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
- occurrence of motif `n' with p-value less than 0.0001.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
Links | Name | Expect | Motifs
|
---|
| BBP_PIEBR
| 4.6e-73
|
|
| ICYA_MANSE
| 1.4e-70
|
|
| RETB_BOVIN
| 3.8e-18
|
|
| LACB_BOVIN
| 0.037
|
|
| MUP2_MOUSE
| 0.3
|
|
SCALE
|
| |
| |
| |
| |
| |
| |
| |
| |
1 |
25 |
50 |
75 |
100 |
125 |
150 |
175 |
|
---|
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
- the motif number of the occurrence,
- the position p-value of the occurrence,
- the best possible match to the motif, and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
BBP_PIEBR
LENGTH = 173 COMBINED P-VALUE = 9.18e-74 E-VALUE = 4.6e-73
DIAGRAM: 3-[1]-66-[2]-34
[1]
1.9e-32
HDGRCPDVKPVDNFDWSRFAGTWWEIAK
++++++++++++++++++++++++++++
1 NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYP
[2]
1.4e-48
VFWVLATDNKNYIIGYNCDYDPDKKGHQDHVWILSRSKVLEG
++++++++++++++++++++++++++++++++++++++++++
76 VGDSKIGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
ICYA_MANSE
LENGTH = 189 COMBINED P-VALUE = 2.81e-71 E-VALUE = 1.4e-70
DIAGRAM: 4-[1]-69-[2]-46
[1]
2.6e-29
HDGRCPDVKPVDNFDWSRFAGTWWEIAK
++++++++++++++++++++++++++++
1 GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNSFVSNGVKEYMEGDLE
[2]
2.6e-49
VFWVLATDNKNYIIGYNCDYDPDKKGHQDHVWILSRSKVLEG
++++++++++++++++++++++++++++++++++++++++++
76 IAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
RETB_BOVIN
LENGTH = 183 COMBINED P-VALUE = 7.60e-19 E-VALUE = 3.8e-18
DIAGRAM: 1-[1]-154
[1]
8.9e-22
HDGRCPDVKPVDNFDWSRFAGTWWEIAK
++++ +++++++++++++++++++++++
1 ERDCRVSSFRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVG
LACB_BOVIN
LENGTH = 178 COMBINED P-VALUE = 7.40e-03 E-VALUE = 0.037
DIAGRAM: 12-[1]-138
[1]
5.0e-05
HDGRCPDVKPVDNFDWSRFAGTWWEIAK
+ + +++++ +
1 MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQ
MUP2_MOUSE
LENGTH = 180 COMBINED P-VALUE = 6.09e-02 E-VALUE = 0.3
DIAGRAM: 180
Debugging Information
CPU: chromo
Time 0.060000 secs.
mast meme.lipocalin.tcm.4.Linuxx86_64.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information