Search for weight matrix patterns of plant regulatory sequences

The program for site search in DNA sequences by score matrices.

The program's brief description.

ScanWM-PL is a program that search for motifs in "+" and "-" strands of DNA using score matrices. The program takes DNA sequences one by one from FASTA file, takes matrices from the score matrices file and annotates DNA sequences by finding motifs (potential sites for binding of transcription factors) in accordance to score matrices. Nucleotide sequences are referred to as motifs (potential sites for binding of transcription factors) if their score is more or equal to "cut-off value" of score matrix; at that the score of sequence is calculated as sum of its nucleotides' score, and the score of a nucleotide in appropriate position is defined in accordance to score matrix. Since ScanWM works with score matrices, elements of which are "log likelihood ratios", the summation is used at sequence score detection.

ScanWM-PL description

ScanWM-PL parameters