ACGTN 500

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.

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.

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 please access http://localhost:8080/meme_5.0.3/doc/mcast-output-format.html.
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 |
Max Combined Motif Width |
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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