Algorithm for Sequence Analysis in Bioinformatics

ESCI-BDIB

Cedric Notredame





OBJECTIVES

An intermediate level course on algorithms in bioinformatics. We will use it to explain common concepts in sequence analysis, starting from the biological relevance of sequence alignment and making our way through the most commonly used algorithms, including Needleman and Wunsch, Smith and Waterman for pairwise alignments, BLAST for database searches, Nussinov for RNA folding and the progressive multiple alignment.



Send your Questions to: cedric.notredame@crg.eu



DateLocationSessionTitleLinks
Lecture 1 - 15/01/21 - 17:30ASABLECTUREPairwise comparisons in an evolutionary context 1: Introduction (37 min) Slides Voiceover
Lecture 1 - 15/01/21 - cont.ASABLECTUREPairwise comparisons in an evolutionary context 2: Notions of molecular evolution (1) (44 min) Slides Voiceover
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Lecture 2 - 19/01/21 - 17:30ASABLECTUREPairwise comparisons in an evolutionary context 3: Notions of molecular evolution (2) (28 min) Slides Voiceover
Lecture 2 - 19/01/21 - cont.ASABLECTUREPairwise comparisons in an evolutionary context 4: Substitution Matrices (37 min) Slides Voiceover
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Lecture 3 - 26/01/21 - 17:30ASABLECTUREPairwise comparisons in an evolutionary context 5: Twilight zone (37 min) Slides Voiceover
Lecture 3 - 26/01/21 - cont.ASABLECTUREPairwise comparisons in an evolutionary context 6: Sequence comparison (14 min) Slides Voiceover
Lecture 3 - 26/01/21 - cont.ASABLECTUREPairwise comparisons in an evolutionary context 7: Interactive Wrap up (30 min)
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Lecture 4 - 02/02/21 - 17:30ASABLECTUREIntroduction to Dynamic Programming 1: Needlman and Wunsch (46 min) Slides Voiceover
Lecture 4 - 02/02/21 - cont.ASABLECTUREIntroduction to Dynamic Programming 2: Smith and Waterman (40 min) Slides Voiceover
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Lecture 5 - 09/02/21 - 17:30ASABLECTUREIntroduction to Dynamic Programming 3: Myers and Millers (26 min) Slides Voiceover
Lecture 5 - 09/02/21 - cont.ASABLECTUREIntroduction to Dynamic Programming 4: interactive wrap up (30 min)
Lecture 5 - 09/02/21 - cont.ASABLECTUREBlast Algorithm 1: Algorithm and Statistics (41 min) Slides Voiceover
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ASABExamLECTURE:PARTIAL EXAM 16/02/21 - 17:30
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Lecture 6 - 23/02/21 - 17:30ASABLECTUREBlast Algorithm 2: Applications and PSI Blast (49 min) Slides Voiceover
Lecture 6 - 23/02/21 - cont.ASABLECTUREIntroduction to Multiple Sequence Alignment 1: MSA usage Overview (40 min) Slides Voiceover
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Lecture 7 - 02/03/21 - 17:30ASABLECTUREIntroduction to Multiple Sequence Alignment 2: Progressive Algorithm (31 min) Slides Voiceover
Lecture 7 - 02/03/21 - cont.ASABLECTUREIntroduction to Multiple Sequence Alignment 3: Interactive Wrap up (30 min)
Lecture 7 - 02/03/21 - cont.ASABLECTURERNA Folding Algorithms 1: Introduction (37 min) Slides Voiceover
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Lecture 8 - 09/03/21 - 17:30ASABLECTURERNA Folding Algorithms 2: Nussinov and Zuker Algorithm (38 min) Slides Voiceover
Lecture 8 - 09/03/21 - cont.ASABLECTURERNA Folding Algorithms 3: Context Free Grammars (25 min) Slides Voiceover
Lecture 8 - 09/03/21 - cont.ASABLECTURERNA Folding Algorithms 4: CYK algorithm (22 min) Slides Voiceover
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REFERENCES

1. Algorithms: Durbin et al., Biological Sequence Analysis, 1999, Oxford Press

2. Bioinformatics Algorithms 1st Edition Design and Implementation in Python

3. Algorithms: Python for Biologists: A complete programming course for beginners, Martin Jones,2013 , Createspace Independent Publishing Platform

4. Evolution: Pathy, Protein Evolution, 2007, Blackwell



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