MOTIVATION Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, C(*)1 and C(S)1, extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequenc...

Biologists highly rely on good algorithms to find the homologous regions in bimolecular sequences. One advanced homology search program, PatternHunter, has been developed in 2002. Unlike the well-known program Blast using a consecutive model, it benefited from gapped (nonconsecutive) model to work better. By observing and analyzing some significant properties of gapped-models, we propose a new ...

We consider the problem of computing a global alignment between two or more sequences subject to varying mismatch and indel penalties. We prove a tight 3(n=2 )+O(n log n) bound on the worst-case number of distinct optimum alignments for two sequences of length n as the parameters are varied. This re7nes a O(n) upper bound by Gus7eld et al., answering a question posed by Pevzner and Waterman. Ou...