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2 Οκτ 2013 (πριν από 3 χρόνια και 9 μήνες)

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M.M. Dalkilic, PhD

Monday, September 08, 2008

Class V

Indiana University, Bloomington, IN

Sequence Homology

1

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

Outline


New Programming Assignment and homework will be
posted today


New Reading Posted on Website


Readings [R] Chaps 5


Most Important Aspect of Bioinformatics

homology search
through sequence similarity (cont’d)


Sequence Alignment (Theoretical)


Sequence Alignment (Practical) FASTA and BLAST


Quick detour first


2

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

Brief Review of Probability


Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

3

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

4

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

5

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

6

We know from the previous slides that
P
is a measure over a Boolean algebra.

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

7

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

8

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

9

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

10

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

11

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

12

Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

13

Odds or (subjective probability) play a significant role in bioinformatics

We either have “odds for (or on)” or “odds against”



Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

14

Increasing information about an event can lead to a change in probability

since, for some, a probability is a degree of belief…Bayesians.



Review cont’d

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

15

FASTA and BLAST

Dot Plots

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

16


Simplest means of comparing two sequences


Visualization is easy to understand

can be the basis for
explaining both FASTA and BLAST


A 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 Plots

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

17


A 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 Plots

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

18


A 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 Matrix

Noise or possible

motifs separated by

gaps

Dot Plots

Sequence Similiarty (Computation) M.M. Dalkilic, PhD
SoI Indiana University, Bloomington, IN 2008 ©

19

Learn to read plots
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