A standard multiple alignment program

A standard multiple alignment program - A standard multiple...

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A standard multiple alignment program: ClustalW From what we have learned in previous sections, doing a simultaneous N-wise alignment is not a realistic option if we have, say, 50 sequences to align. What to do? The obvious alternative is to use a so-called progressive alignment method : The alignment is built up in stages where a new sequence is added to an existing alignment, using some rules to determine in which order the sequences should be added, and how. ) is one of the standard programs implementing one variant of the progressive method in wide use today for multiple sequence alignment. The W denotes a specific version that has been developed from the original Clustal program. The basic steps of the algorithm implemented in ClustalW are: 1. Compute the pairwise alignments for all against all sequences. The similarities are stored in a matrix (sequences versus sequences). 2. Convert the sequence similarity matrix values to distance measures, reflecting evolutionary distance between each pair of sequences. 3. Construct a tree (the so-called guide tree ) for the order in which pairs of sequences are to be aligned and combined with previous alignments. This is done using a neighbour-joining clustering algorithm. In the case of ClustalW, a 4.
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This note was uploaded on 11/22/2011 for the course CHEMISTRY CHM1025 taught by Professor Laurachoudry during the Fall '10 term at Broward College.

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A standard multiple alignment program - A standard multiple...

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