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 "@sequence_filename@" was supplied to MCAST.

Sequence Count Residue Count
@num_sequences@ @num_residues@

Motifs

The following motifs were supplied to MCAST from "@pattern_filename@"

@motif_list@
Motif Width Best possible match Best possible RC match

Search Results

Top

Top Scoring Matches

@results@
Top
MCAST version
@version@ (Release date: @release_date@)
Command line summary

Background letter frequencies (from @bg_source@):
@background_freqs@

@computation_time@

Explanation of MCAST Results

Top

The MCAST results consist of

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.
&more;
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.
@mcast_match_data@