MSA-align2 - Multiple Alignment Stuart M. Brown NYU School...

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Multiple Alignment Stuart M. Brown NYU School of Medicine
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Pairwise Alignment The alignment of two sequences (DNA or protein) is a relatively straightforward computational problem. The best solution seems to be an approach called Dynamic Programming.
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Dynamic Programming Dynamic Programming is a very general programming technique. It is applicable when a large search space can be structured into a succession of stages, such that: the initial stage contains trivial solutions to sub-problems each partial solution in a later stage can be calculated by recurring a fixed number of partial solutions in an earlier stage the final stage contains the overall solution
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Global vs. Local Alignments Global alignment algorithms start at the beginning of two sequences and add gaps to each until the end of one is reached. Local alignment algorithms finds the region (or regions) of highest similarity between two sequences and build the alignment outward from there.
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GAP The GCG program GAP implements the Needleman and Wunsch Global alignment algorithm. Global algorithms are often not effective for highly diverged sequences and do not reflect the biological reality that two sequences may only share limited regions of conserved sequence. Sometimes two sequences may be derived from ancient recombination events where only a single functional domain is shared. GAP is useful when you want to force two sequences to align over their entire length
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BESTFIT The GCG program BESTFIT implements the Smith-Waterman local alignment algorithm. FASTA and BLAST are local alignment algorithms NCBI has a “BLAST 2 Sequences” feature on its website: http://www.ncbi.nlm.nih.gov/gorf/bl2.html
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Pairwise Alignment on the Web The ALIGN global alignment program is available at several servers: http://molbiol.soton.ac.uk/compute/align.html http://www2.igh.cnrs.fr/bin/align-guess.cgi LALIGN local alignment program is available at several servers: http://www2.igh.cnrs.fr/bin/lalign-guess.cgi http://www.ch.embnet.org/software/LALIGN_form.html LFASTA uses FASTA for local alignment of 2 sequences: http://pbil.univ-lyon1.fr/lfasta.html BLAST 2 Sequences (NCBI) http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
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In theory, making an optimal alignment between two sequences is computationally straightforward (Smith- Waterman algorithm), but aligning a large number of sequences using the same method is almost impossible. The problem increases exponentially
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This note was uploaded on 02/13/2012 for the course CS 91.510 taught by Professor Staff during the Fall '09 term at UMass Lowell.

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MSA-align2 - Multiple Alignment Stuart M. Brown NYU School...

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