Motif ClusterAlignment and Search Tool (MCAST)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

Inputs   |   Search Results   |   Program information   |   Documentation

Inputs

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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 AATTGTGACGTTGTTCAC GTGATCTACGTCACAATT
2 8 CGGTGGGG CCCCGCCG
3 11 CCTGGTGTGCC GGGACCCCAGG

Search Results

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Top Scoring Matches

Each of the following 17 matches has a q-value less than .
The motif matches shown have a position p-value less than .
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 17.8792 -- -- --    
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trn9cat 36 102 10.9305 -- -- --    
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ilv 5 61 9.60584 -- -- --    
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ara 59 77 7.17504 -- -- --    
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male 14 49 6.74549 -- -- --    
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malt 41 59 6.51379 -- -- --    
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deop2 60 78 5.24387 -- -- --    
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pbr322 57 75 4.32247 -- -- --    
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uxu1 17 35 4.08176 -- -- --    
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ce1cg 65 83 3.76129 -- -- --    
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tnaa 75 93 2.964 -- -- --    
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gale 46 64 2.964 -- -- --    
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crp 67 85 2.46002 -- -- --    
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cya 50 68 2.2681 -- -- --    
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ompa 48 66 1.79464 -- -- --    
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tdc 82 100 1.73904 -- -- --    
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malk 61 79 1.5644 -- -- --    
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MCAST version
4.8.0 (Release date: 7 EST 20)
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.
Command line summary

Background letter frequencies (from non-redundant database):
A: 0.282   C: 0.222   G: 0.229   T: 0.267

show model parameters...

Explanation of MCAST Results

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The MCAST results consist of

Inputs

MCAST received the following inputs.

Sequence Databases

This table summarises the sequence databases specified to MAST.

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 MAST.

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 MAST 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.
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