Threshold for Positional Weight Matrix

13 years 6 months ago
Threshold for Positional Weight Matrix
In biological sequence research, the positional weight matrix (PWM) is often used to search for putative transcription factor binding sites. A set of experimentally verified oligonucleotides known to be functional motifs are collected and aligned. The frequency of each nucleotide A, C, G, or T at each column of the alignment is calculated in the matrix. Once a PWM is constructed, it can be used to search from a nucleotide sequence for subsequences that can possibly perform the same function. The match between a subsequence and a PWM is usually described by a score function, which measures the closeness of the subsequence to the PWM as compared with the given background. Nevertheless, the score function is usually motif-length-dependent and thus there is no universally applicable threshold. In this paper, we propose an alternative scoring index (G) varying from zero, where the subsequence is not much different from the background, to one, where the subsequence fits best to the PWM. We a...
Yunlian Pan, Sieu Phan
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2008
Where ENGL
Authors Yunlian Pan, Sieu Phan
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