{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

MSA-align2

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

This preview shows pages 1–13. Sign up to view the full content.

Multiple Alignment Stuart M. Brown NYU School of Medicine

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
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.

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
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

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
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.
QuickTimeﾪ and a TIFF (Uncompressed) decompressor are needed to see this picture.

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
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
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

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
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

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
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
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

### Page1 / 33

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

This preview shows document pages 1 - 13. Sign up to view the full document.

View Full Document
Ask a homework question - tutors are online