Bioinformatics tools in protein sequence and structure analysis

This theoretical and practical course will introduce the use of bioinformatics tools for retriving, comparing, visualizing and analyzing protein sequences and structures. Applicant should have a good practice in internet browsing on computer, and a bachelor grade (M1) or training in molecular biology and protein biochemistry. No skill in computer programming will be required.

Sequence search in public databases (BLAST, PSI-BLAST, PHI-BLAST, HMMsearch). Search from fuzzy patterns (Motif). Sequence alignment (Align, Alix, ClustalW/X, 3D-Coffee). Sequence profil and consensus from sequence subsets (Jalview, Logo,HMMer). Logical operation, auto and crosscorrelation on sequence subsets (Evoluswap). Search for signal peptide (SignalP), transmembrane domain (TMHMM), glycosylation sites, acylation sites, phosphorylation sites, functional signature (Prosite). Secondary and tertiary structure prediction (Psi-pred, SCWRL, Swiss-model, Modeller, Robetta). 3D-model validation (Colorado3D). Display residue conservation over structure and analysis of residues programming for fold or function (Colorado3D). Search for ligand binding sites (SUMO).

Each student will have a computer. All exercices and corrections will be accessible online on the course web site.

Validations :

A diploma will be delivered by the Institut Pasteur to students who will succeed to the final exam,
Doctoral School Modules.

• Full time , from June 24 to 29, 2013

• Nomber of students : 16

• Registration deadline: April 1, 2013

  Tuition fees

Members of Course commitee:

O. Ozier-Kalogéropoulos (Institut Pasteur), C. Parsot (Institut Pasteur), *(Université P. et M. Curie),  *(Université Paris-Diderot) et Thierry Rose (Institut Pasteur).