Bioinformatics PhD. Course

1
Bioinformatics PhD. Course
Summary (approximate)

• 1. Biological introduction

• 2. Comparison of short sequences (lt10.000 bps)

• 3 Comparison of large sequences (up to 250 000
  000)

• 4 Sequence assembly

• 5 Efficient data search structures and algorithms

• 6 Proteins...

2
2. Comparison of short sequences (lt10.000 bps)
Summary (more or less)

• 2.1 Dot matrix
• 2.2 Pairwise alignment.
• 2.3 Hash algorithms.
• 2.4 Multiple alignment.

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2. Dot matrix
Given two sequences, how we can analyse their
degree of identity?
By searching those parts that match
1/0
1 if both characters coincide
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2. Dot matrix
Given two sequences, how we can analyse their
degree of identity?
By searching those parts that match
5
2.1 Dot matrix
Lwindow length
What is the cost of the algorithm?
When are the matchings relevant?
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2.1. Dot matrix algorithm cost

• long(S1)long(S2) L in other words O(n2
  L)

• can long(S1)long(S2) be possible?
• can we also say that O(n2 ) is independent of L?

7
2.1. Dot matrix signals
A transposons
When are signals statistically significant?
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2.1. Dot matrix statistical significance
We need to define a random model against which
to compare the signals
we define RV X number of characters that
coincide,
then Prob(Xk)comb(L,k) pk (1-p)L-k
What is its expected value?