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. The practicals will be in Python and will involve driving the students through an implementation of these algorithms. The biobliography is given by order of importance.




REQUISITES

Practicals will be in python 2.7. They will involve adapting existing scripts rather than programming from scratch. For this reason, students with no practical knowledge of python but with a good grasp of programming languages like Perl, C or JAVA should manage reasonnably well. Students are expected to bring their own lap-top and advised to have a LINUX boot though Virtual MAchine support will be provided.



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



DateLocationSessionTitleLinks
14/01/20 - 17:30ASABLECTURE1-Pairwise comparisons in an evolutionary contextL
17/01/20 - 15:00ASABLECTURE2-Substitution MatricesL
24/01/20 - 15:00ASABLECTURE3-Introduction to Dynamic Programming-1L
31/01/20 - 15:00ASABLECTURE4-Introduction to Dynamic Programming-2L
07/02/20 - 15:00ASABLECTUREMid Term Exam
14/02/20 - 15:00ASABLECTURE5-Blast AlgorithmL
21/02/20 - 15:00ASABLECTURE6-Introduction to Multiple Sequence AlignmentL
28/02/20 - 15:00ASABLECTURE7-Multiple Sequence Alignment AlgorithmsL
06/03/20 - 15:00ASABLECTURE8-RNA Folding AlgorithmsL
.
.
21/01/20 - 17:30ASABPRACTICALS1-Parsing Biological FilesP
28/01/20 - 17:30ASABPRACTICALS2-Computing Substitution MatricesP
04/02/20 - 17:30ASABPRACTICALS3-Introduction to Dynamic Programming 1P
11/02/20 - 17:30ASABPRACTICALS4-Introduction to Dynamic Programming 2P
18/02/20 - 17:30ASABPRACTICALS5-Parsing and manipulating binary treesP
25/02/20 - 17:30ASABPRACTICALS6-Implementing your own multiple sequence alignerP
03/02/20 - 17:30ASABPRACTICALS7-Project PreparationP
10/03/20 - 17:30ASABPRACTICALS8-Project PresentationP
.



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



This Entire Course Was Automatically Generated Using BED, the Bioinformatics Exercise Database. BED is a freeware available on request Cedric Notredame