# 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.nbcr.net.

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]

Inputs | Search Results | Program information | Documentation

## Inputs | Top

#### Sequence Database

The sequence database "crp0.s" was supplied to MCAST.

Sequence Count | Residue Count
--- | ---
18 | 1890

#### Motifs

The following motifs were supplied to MCAST from "crp0.meme.html"

Motif | Width | Best possible match | Best possible RC match
1 | 18 | A A T T G T G A C G T T G T T C A C | G T G A T C T A C G T C A C A A T T
2 | 8 | C G G T G G G G | C C C C G C C G
3 | 11 | C C T G G T G T G C C | G G G A C C C C A G G

## Search Results | Top

#### Top Scoring Matches

Each of the following 17 matches has a q-value less than 1.
The motif matches shown have a position p-value less than 0.0005.
Click on the arrow (↧) next to the block diagram to view more information about a sequence.

| Motif 1

| Motif 2

| Motif 3

| Sequence | Start | Stop | Score | p-value | E-value | q-value |  |
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| lac | 9 | 44 | 21.8027 | -- | -- | --
↧ | + -
| trn9cat | 36 | 102 | 14.4848 | -- | -- | --
↧ | + -
| ilv | 5 | 61 | 12.6927 | -- | -- | --
↧ | + -
| ara | 59 | 77 | 10.0989 | -- | -- | --
↧ | + -
| male | 14 | 49 | 9.85931 | -- | -- | --
↧ | + -
| malt | 41 | 59 | 9.5075 | -- | -- | --
↧ | + -
| deop2 | 60 | 78 | 8.23625 | -- | -- | --
↧ | + -
| pbr322 | 57 | 75 | 7.21464 | -- | -- | --
↧ | + -
| uxu1 | 17 | 35 | 7.10103 | -- | -- | --
↧ | + -
| ce1cg | 17 | 83 | 6.84723 | -- | -- | --
↧ | + -
| gale | 46 | 64 | 6.07963 | -- | -- | --
↧ | + -
| tnaa | 75 | 93 | 5.86876 | -- | -- | --
↧ | + -
| crp | 67 | 85 | 5.50862 | -- | -- | --
↧ | + -
| cya | 50 | 68 | 5.28224 | -- | -- | --
↧ | + -
| ompa | 48 | 66 | 5.036 | -- | -- | --
↧ | + -
| malk | 61 | 79 | 4.98687 | -- | -- | --
↧ | + -
| tdc | 82 | 100 | 4.60501 | -- | -- | --
↧ | + -

Top

##### MCAST version

4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000)

##### Command line summary

mcast -oc mcast_example_output_files crp0.meme.html crp0.s
Background letter frequencies (from non-redundant database):
A: 0.282 C: 0.222 G: 0.229 T: 0.267
show model parameters...
hide model parameters...

## Explanation of MCAST Results | Top

#### The MCAST results consist of

- The inputs to MCAST including:
  1. The sequence database showing the sequence and residue counts. [View]
  2. The motifs showing the name, width, and best scoring match [View]
- The search results showing top scoring sequences with tiling of all of the motifs matches shown for each of the sequences. [View]
- The program details including:
  1. The version of MCAST and the date it was released. [View]
  2. The command line summary detailing the parameters with which you ran MCAST. [View]
- This explanation of how to interpret MCAST results.

#### Inputs

MCAST received the following inputs.

##### Sequence Databases

This table summarises the sequence databases specified to MCAST.

Database
  The name of the database file.
Sequence Count
  The number of sequences in the database.
Residue Count
  The number of residues in the database.

##### Motifs

Summary of the motifs specified to MCAST.

Name
  The name of the motif. If the motif has been removed or removal is recommended to avoid highly similar motifs then it will be displayed in red text.
Width
  The width of the motif. No gaps are allowed in motifs supplied to MCAST as it only works for motifs of a fixed width.
Best possible match
  The sequence that would achieve the best possible match score and its reverse complement for nucleotide motifs.

#### Search Results

MCAST provides the following motif search results.

##### Top Scoring Sequences

This table summarises the top scoring sequences. The sequences are sorted by the Sequence q-value from most to least significant.

Sequence
  The name of the sequence. This maybe be linked to search a sequence database for the sequence name.
Start
  The position of the start of the match in 1-based coordinates, starting at the first position in the sequence.
Stop
  The position of the end of the match in 1-based coordinates, starting at the first position in the sequence.
Score
  The MCAST score for the match.
p-value
  The p-value of the match score.
E-value
  The E-value of the match score.
q-value
  The q-value of the match score.
↧
  Click on this to show additional information about the sequence such as a description, combined p-value and the annotated sequence.
Block Diagram
  The block diagram shows the best non-overlapping tiling of motif matches on the sequence.
  - The length of the line shows the length of a sequence relative to all the other sequences.
  - A block is shown where the positional p-value of a motif is less (more significant) than the significance threshold which is 0.0001 by default.
  - If a significant motif match (as specified above) overlaps other significant motif matches then it is only displayed as a block if its positional p-value is less (more significant) then the product of the positional p-values of the significant matches that it overlaps.
  - The position of a block shows where a motif has matched the sequence.
  - The width of a block shows the width of the motif relative to the length of the sequence.
  - The colour and border of a block identifies the matching motif as 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 positional p-value, truncated at the height for a p-value of 1e-10.
  - Hovering the mouse cursor over the block causes the display of the motif name and other details in the hovering text.
  - DNA only; blocks displayed above the line are a match on the given DNA, whereas blocks displayed below the line are matches to the reverse-complement of the given DNA.
  - DNA only; when strands are scored separately then blocks may overlap on opposing strands.

ACGTN