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Motif >motif1 atgc >motif2 atgc all sequences should have the same length

Sequence(s) to scan E. coli entire chromosome Escherichia coli K-12 (strain MG1655) sequence and annotations were taken from the sequencing project at the University of Wisconsin, Madison. E. coli operon upstream regions An upstream region was taken for a coding sequence if it is the first gene in the operon or follows an annotated promoter. Upstream regions contain between 50 and 600 nucleotides (uppercase) plus 20 nucleotides extending into the coding region (lowercase). Each upstream region is labeled with genes downstream in the same operon. Specified below >seq1 atgc >seq2 atgc

Negative examples (optional) each sequence contributes a single negative example – its highest scoring site

Method Basic Method: Centroid PSSM Berg & von Hippel Consensus   Scope: Single column Adjacent pairs 2 3 4 Full scope Use information content

Criteria Top:     report top n scoring sites Cutoff: report sites with score >= cutoff P-value: choose a cutoff so that P[score >= cutoff] = pvalue for a randomly generated sequence of the same length as the motif Rank: report sites that score higher than the nth negative example False-Positive Rate: choose a cutoff with an acceptable false-positve rate. specifically, a cutoff so that P[neg >= cutoff] = rate rank and false-positive criteria require negative examples use '$1','$2',... to read the value from the sequence description (at the specified position)

Please email questions or comments to msingh at lists.cs.princeton.edu

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