ACGTN 500

The name of the motif.

The alternate name of the motif.

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]

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## Search Results

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#### Top Scoring Clusters

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## Inputs & Settings

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#### Alphabet

#### Sequences

The following sequence databases were supplied to MCAST.

Database | PSP/Wig file | PSP Distribution file | Sequence Count | Letter Count
--- | --- | --- | --- | ---

#### Motifs

The following motif databases were supplied to MCAST.

Database

Which contained the following motifs.

#### Other Settings

Alpha |
Hard mask |
Max Gap |
Max Stored Scores |
Motif p-value threshold |
Output Threshold | ≤
Parse Genomic Coordinates |
Synthetic Scores |
Min Match Score |
Cost Factor |
Gap Open Cost |
Gap Extend Cost |

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##### MCAST version

(Release date: )

##### Reference

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]

##### Command line summary

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