Jing, Junmei; Wilson, Susan; Burden, Conrad
The use of k-word matches was developed as a fast alignment-free comparison method for dna sequences in cases where long range contiguity has been compromised, for example, by shuffling, duplication, deletion or inversion of extended blocks of sequence. Here we extend the algorithm to amino acid sequences. We define a new statistic, the weighted word match, which reflects the varying degrees of similarity between pairs of amino acids. We computed the mean and variance, and simulated the...[Show more]
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