This pseudocount value is added to each of the motif's letter counts in proportion to the background frequency before generating the postion specific scoring matrices.

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This value sets the scale for calculating p-scores of motif hits. Hit p-values below this threshold get positive scores while hit p-values above this threshold get negative scores.

The p-score S for a hit with p-value p is:
S = -log2(p / hit p-value threshold)

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This value specifies the longest distance allowed between two hits in a match. Hits separated by more than this value will be placed in different matches.

Large values for this field combined with large values for the hit p-value threshold may prevent MCAST from computing E-values.

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This value sets the E-value threshold for displaying search results. If the E-value of a match is greater than this value, then the match will not be included in the output.

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MCAST - Motif Cluster Alignment and Search Tool
../doc/images/mcast_icon.png: MCAST Logo

Data Submission Form

Scan sequences for clusters of motifs.

motifs Input the motifs DNA RNA FILE register_component sequences Input the sequences DNA RNA DATABASE register_component

What pseudocount should be added to motifs?

What p-value threshold should be used for scoring motif hits?

How far apart can adjacent motif hits be spaced?

How should matches be filtered before output?