{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

pairwise-alignment-2

pairwise-alignment-2 - Pairwise Sequence...

Info icon This preview shows pages 1–4. Sign up to view the full content.

View Full Document Right Arrow Icon
Pairwise Sequence Alignment (Continued) BMI/CS 576 www.biostat.wisc.edu/bmi576/ Mark Craven [email protected] Fall 2011 Local alignment so far we have discussed global alignment , where we are looking for best match between sequences from one end to the other often we want a local alignment , the best match between subsequences of x and y
Image of page 1

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

View Full Document Right Arrow Icon
Example local alignment aligning my name against the sequence for dTDP-4-dehydrorhamnose reductase from the bacterium opitutus terrae …LSGAYHLAASGHTSWHGFASAIIDLMPLD ARKCRAVE AIT… M ARKCRAVE N Local alignment motivation useful for comparing protein sequences that share a common motif (conserved pattern) or domain (independently folded unit) but differ elsewhere useful for comparing DNA sequences that share a similar motif but differ elsewhere useful for comparing protein sequences against genomic DNA sequences (long stretches of uncharacterized sequence) more sensitive when comparing highly diverged sequences
Image of page 2
Local alignment DP algorithm original formulation: Smith & Waterman, Journal of Molecular Biology , 1981 interpretation of array values is somewhat different: F ( i, j ) = score of the best alignment of a suffix of x [1… i ] and a suffix of y [1… j ] Local alignment DP algorithm F ( i , j ) = max F ( i " 1, j " 1) + s ( x i , y j ) F ( i " 1, j ) " d F ( i , j "
Image of page 3

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

View Full Document Right Arrow Icon
Image of page 4
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern