Biological Sequences Analysis, spring semester 2009, MTA

Overview:

The course gives an introduction to the field of sequence analysis in bioinformatics.
During the course various approaches for sequence analysis, and corresponding tools will be taught.

Teaching instructors: Ofir Cohen and Dudu Burstein.

Course hours: Wednesdays, 10:00 - 11:45.

Check out the updated syllabus

Announcements:

24.5 - Exercise 2 should be submitted not later than 03/06/2009.
Please go over the exercise and we will answer any questions during the next lesson.

21.4 - The 22th April talk: finish with Phylogenetic trees (previous lesson) followed by Detecting selection using phylogeny. The lesson will be with no intermission- 10:00-11:30

18.3 - Course hours changed: Early start 10:00 (and early end).

18.3 - Exercise 1 due date: 8 April (this is for real).

Course materials:

Class Date Topic Presentation Assignments Useful stuff
Lesson 1 04.03.2009  Computational biology -
 revolutionizing science at the turn of the century		 1Revolution.ppt    
Lesson 2 11.03.2009  Pairwise alignment 2pairwise_alignment.ppt   NeedlemanWunsch.ppt
Exercise 1 18.03.2009  Databases and BLAST 1Databases_and_Blast.ppt HW1  
Lesson 3 25.03.2009  Multiple Sequence Alignment & Hidden Markov Models 3MSAs and HMMs.ppt   notes
Lesson 4 01.04.2009  Phylogenetic trees -
 The evolutionary metaphor and paradigm 		4_phylogeny.ppt    
Lesson 5 22.04.2009  Detecting selection using phylogeny -
 +finish Phylogeny 		5_Detecting_selection_using_phylogeny.ppt    
Exercise 2 06.05.2009  MSA, phylogeny and selection detection ex2_msa_phylogeny_selection.ppt HW2 due on 03/06 MidTerm example questions
NJplot ClustalX globin.fasta, pp2c.aln, 1t82.aln
Lesson 6 19.05.2009  Gene Expression and PPI 6_GeneExpression_PPI.ppt
6.5E-Predict.ppt 		  Microarray on YouTube
Video on Solexa (deep sequencer)
Lesson 7 27.05.2009  inside The Genome 7_insideTheGenome.ppt    
Exercise 3 03.06.2009  Protein Motifs and Genome Browser ex3_Prosite_UCSC.ppt HW3 due on 17/06  
Lesson 8 10.06.2009  Machine Learning (and the Legionella example) 8_MachineLearningLegion.ppt    
Lesson 9 17.06.2009  networks & Systems Biology 9_networks.ppt    


Database or application name Contents URL
NCBI Sequences, structures, diseases, publications, and more http://www.ncbi.nlm.nih.gov
EMBL-EBI Data resources and tools http://www.ebi.ac.uk
PubMed Biomedical publications http://www.ncbi.nlm.nih.gov/pubmed
Google scholar Publications http://scholar.google.co.il
Swiss-Prot Protein knowledgebase http://www.expasy.ch/sprot
PDB Database of biological macromolecules http://www.rcsb.org/pdb/home/home.do
GO Gene ontology database http://www.geneontology.org
NCBI BLAST All BLAST tools http://blast.ncbi.nlm.nih.gov/Blast.cgi
EMBL-EBI ClustalW An interface to a multiple sequence alignment program http://www.ebi.ac.uk/Tools/clustalw2
PhyML An interface to a phylogeny reconstruction program http://atgc.lirmm.fr/phyml
Prosite Database of protein domains, families, and functional sites http://www.expasy.org/prosite
UCSC Genome browser http://genome.ucsc.edu
Ensembl Genome browser http://www.ensembl.org
ConSeq A server for the identification of functionally and structurally important residues in protein sequences http://conseq.tau.ac.il
ConSurf A server for the identification of functionally and structurally important residues in protein structures http://consurf.tau.ac.il
Selecton A server for the identification of site-specific positive selection & purifying selection http://selecton.tau.ac.il
DALI Distance matrix ALIgnment http://ekhidna.biocenter.helsinki.fi/dali_server