dscan

dscan searches a database for sites matching a specific model.
Neuwald, Liu and Lawrence, Gibbs motif sampling, Protein Science (1995) 4:1618-1632

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Email Address
Program to be run *
Sequences to be searched (in FASTA format) *
Scan E. coli intergenic regions (This may be slow to load)
Scan R. palustris intergenic regions (This may be slow to load)
Aligned segments from Gibbs or count matrix *
Alphabet and scoring matrix to be used *
Reverse complement search of database file (DNA only)
Maximum E-value detected Default: 0.01
Minimum -log10(p-value) required for each motif Default: 0
Scan for repeats
Maximum # repeats per sequence (use with "scan for repeats") Default: 10
Minimum # repeats per sequence (use with "scan for repeats") Default: 2
Print top values. Ignore "maximum E-value detected"
Require motifs to be in correct order
Don't allow overlapping motifs when using multiple models
Alternate Bonferroni adjustment for the size of the database
One model only
Shuffle input sequences
Sample output

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