MCAST - Submission form

Checking this box instructs MCAST to mask all lower-case nucleotides in the input sequences by converting them to the 'N' character. This is done by default, so you must un-check the box if you do not want lower-case nucleotides to be masked.

Note: Leaving this box checked is STRONGLY advised when scanning one of the built-in DNA databases as repetitive DNA regions have been marked using lower-case via the RepeatMasker tool. Un-checking this box can result in many FALSE POSITIVE results in repetitive DNA regions.

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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_ALPHABET FILE register_component sequences Input the sequences DNA_ALPHABET DATABASE register_component

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

Hit p-value <

### How far apart can adjacent motif hits be spaced?

Spacing ≤

### How should matches be filtered before output?

Match E-value <

### Should lower-case nucleotides be masked?

convert lower-case nucleotides to 'N'