The width of the motif. No gaps are allowed in motifs supplied to MCAST
as it only works for motifs of a fixed width.
The name of the (FASTA) sequence database file.
The name of the position specific priors file.
The name of the binned distribution of priors file.
The number of sequences in the database.
The number of letters in the sequence database.
The name of the file containing the (MEME-formatted) motifs used in the search.
The block diagram shows the motif matches comprising a motif cluster detected by MCAST.
Hovering the mouse cursor over a motif match causes the display of the motif name,
position p-value of the match and other details in the hovering text.
Click the small blue arrow on the left of the diagram to see more detail for
a given motif cluster.
A block is shown where the motif is on the
highest-scoring (Viterbi) path of the hidden Markov model
constructed by MCAST contains the motif.
All motif matches have match p-value
less (more significant) than the significance threshold, which is 0.0005 by default.
The position of a block shows where a motif has matched the sequence.
Complementable alphabets (like DNA) only: Blocks displayed above the line are a
match on the given sequence, whereas blocks displayed below the line are matches
to the reverse-complement of the given sequence.
The width of a block shows the width of the motif relative to the length of the
displayed portion of the input sequence.
The color and border of a block identifies the matching motif as in the legend.
Note: You can change the color of a motif by clicking on the motif in the legend.
The height of a block gives an indication of the significance of the match as
taller blocks are more significant. The height is calculated to be proportional
to the negative logarithm of the motif match
p-value,
truncated at the height for a p-value of 1e-10.
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 p-value of a motif match is the probability of a single random
subsequence of the length of the motif
scoring at least as
well as the observed match.
A selected portion of the input sequence with the matching motifs displayed above it.
For each matching motif the strand of the match (+/-),
the consensus sequence of the motif, the p-value of the
individual motif match (see also help button for "Cluster Score") and
the sequence logo of the motif is shown.
You can select the portion of the sequence to be displayed by sliding the
two buttons below the sequence block diagram so that the portion you want
to see is between the two needles attached to the buttons. By default the
two buttons move together, but you can drag one individually by
holding shift before you start the drag.
The name of the alphabet symbol.
The frequency of the alphabet symbol as defined by the background model.
The full sequence identifier.
This lists the name of the sequence, typically the chromosome or contig name.
MCAST was run with --parse-genomic-coord specified and
has split the sequence identifier into sequence name, sequence start and sequence end.
This lists the first genomic offset (1-based) of the displayed region.
MCAST was run with --parse-genomic-coord specified and
has split the sequence identifier into sequence name, sequence start and sequence end in genome coordinates.
This lists the first sequence offset (1-based) of the displayed region.
This lists the last genomic offset (1-based) of the displayed region.
MCAST was run with --parse-genomic-coord specified and
has split the sequence identifier into sequence name, sequence start and sequence end in genome coordinates.
This lists the last sequence offset (1-based) of the displayed region.
The start of the motif cluster relative to the start of the sequence (1-based).
The last position of the motif cluster relative to the start of the sequence (1-based).
The score that the hidden Markov model created by MCAST assigned to the motif cluster.
This is the sum of the scores of the individual motif matches in the cluster, plus a
gap penalty, g, multiplied by the total size of the inter-motif gaps
in the cluster. Individual motif match scores are log2(P(s)/p), where
s is the log-odds score
of the motif match, P(s) is the
p-value
of the motif match, and p is the user-specified
p-value threshold (default: 0.0005).
The p-value of the motif cluster score.
MCAST estimates p-values by fitting an exponential distribution
the observed motif cluster scores.
The E-value of the motif cluster score.
MCAST estimates this by multiplying the
p-value
of the motif cluster score
times the (estimated) number of random matches found in the search.
The q-value of the motif cluster score.
MCAST estimates q-values from the motif cluster score p-values
using the method of Benjamini and Hochberg
(Journal of the Royal Statistical Society B, 57:289-300, 1995).
Motif
1
p-value
8.23e-7
Start
23
End
33
Cluster Start:
Cluster Stop:
Cluster Score:
p-value:
E-value:
q-value:
Annotated Sequence
Change the portion of annotated sequence by dragging the buttons; hold shift to drag them individually.
MCAST
Motif Cluster Alignment and Search Tool
For further information on how to interpret these results or to get a
copy of the MEME software please access
http://meme-suite.org.
If you use MCAST in your research please cite the following paper:
Timothy Bailey and William Stafford Noble,
"Searching for statistically significant regulatory modules",
Bioinformatics (Proceedings of the European Conference on Computational Biology),
19(Suppl. 2):ii16-ii25, 2003.
[full text]
Timothy Bailey and William Stafford Noble,
"Searching for statistically significant regulatory modules",
Bioinformatics (Proceedings of the European Conference on Computational Biology),
19(Suppl. 2):ii16-ii25, 2003.
[full text]
