Sequence Homology
M.M. Dalkilic, PhDMonday, September 08, 2008Class VIndiana
University, Bloomington, INSequence Homology1Sequence Similiarty
(Computation) M.M. Dalkilic, PhD SoI Indiana University,
Bloomington, IN 2008 OutlineNew Programming Assignment and homework
will be posted todayNew Reading Posted on WebsiteReadings [R] Chaps
5Most Important Aspect of Bioinformaticshomology search through
sequence similarity (contd)Sequence Alignment (Theoretical)Sequence
Alignment (Practical) FASTA and BLASTQuick detour first
2Sequence Similiarty (Computation) M.M. Dalkilic, PhD SoI
Indiana University, Bloomington, IN 2008 Brief Review of
ProbabilitySequence Similiarty (Computation) M.M. Dalkilic, PhD SoI
Indiana University, Bloomington, IN 2008 3
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 4
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 5
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 6We know from the
previous slides that P is a measure over a Boolean algebra.
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 7
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 8
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 9
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 10
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 11
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 12
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 13Odds or (subjective
probability) play a significant role in bioinformaticsWe either
have odds for (or on) or odds against
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 14Increasing
information about an event can lead to a change in
probabilitysince, for some, a probability is a degree of
beliefBayesians.
Review contdSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 15
FASTA and BLASTDot PlotsSequence Similiarty (Computation) M.M.
Dalkilic, PhD SoI Indiana University, Bloomington, IN 2008
16Simplest means of comparing two sequencesVisualization is easy to
understandcan be the basis for explaining both FASTA and BLASTA Dot
plot is simply a rectangular grid whose leftmost column and bottom
row are sequences. A box is checked if, for cell i,j, the symbols
match i units from the bottom-to-top and j units from
left-to-rightDot PlotsSequence Similiarty (Computation) M.M.
Dalkilic, PhD SoI Indiana University, Bloomington, IN 2008 17A Dot
plot is simply a rectangular grid whose leftmost column and bottom
row are sequences. A box is checked if, for cell i,j, the symbols
match i units from the bottom-to-top and j units from
left-to-right
Dot PlotsSequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 18A Dot plot is simply
a rectangular grid whose leftmost column and bottom row are
sequences. A box is checked if, for cell i,j, the symbols match i
units from the bottom-to-top and j units from left-to-right
Scoring MatrixNoise or possiblemotifs separated bygaps Dot
PlotsSequence Similiarty (Computation) M.M. Dalkilic, PhD SoI
Indiana University, Bloomington, IN 2008 19
Learn to read plots---
