Then, you build the multiple alignment by first aligning the most closely related pair. So, a quicker algorithm is used.īasically, one aligns each sequence pairwise to every other sequence. Basically, even dynamic programming finds optimal alignment of 10 sequences much over 100 residues long an uncomputably hard problem. CLUSTAL is an example of a heuristic algorithm for progressive multiple alignment. Question 3 deals with material briefly mentioned in the book that can best be found by reading the CLUSTALW manuscript (and the short Clustal 2.0 manuscript). CLUSTALW can be used via the internet or CLUSTALX can be downloaded to your computer. The most widely used multiple alignment algorithim is CLUSTAL, whose current incarnation is CLUSTALX and CLUSTALW. Use tools for viewing multiple sequence alignments. Learn to interpret multiple sequence alignments. Learn to do multiple sequence alignments. ClustalW/X default colors ClustalW original paper ClustalW/X 2.0 paper
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