![]() ![]() CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. ( Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. One of the easiest to use, most sophisticated, and most versatile alignment programs is clustalw Usually global alignme nts are the easiest to calculate (local see below) The so called Needleman-Wunsch algorithm is widely used, it optimizes a positive alignment score, a related (and under some conditions equivalent approach) is to minimize the differences between to sequences. (According to the motto: "It can be easily shown" - see here ). For two sequences it is "easy" to calculate an optimal global alignment. There are many different algorithms to calculate pairwise sequence alignments. The dot intensity is adjusted to reflect the percent identity (or similarity) in the two windows. In more realistic implementations a window of 5 to 20 nucleotides or amino acids is slid along one of the axes (i.e., sequences) and compared to every possible window on the other axis (sequence). In its most straight forward implementation the two sequences to be aligned are written along the coordinate axis. The easiest way to align two sequences is to use a dotplot. ![]()
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