Genomicsa: analysis and algorithms

Jan Pačes

News and changes.

• September 25th: sorry for short notice, I catched something and I can't talk. Instead of lecture, today only exersice with Marharyta, starts at 12.
• October 2nd: canceled due to illness (no lecture, no practical) I believe I'll be OK next week. JP

Who, when, where

• Lecturer: Jan Pačes; Email: hpaces@img.cas.cz; Subject: GAA +info
• Assistance and help: Marharyta Klianitskaya; Email: klianitm@vscht.cz
• Location: B1322, VŠCHT B, entrance from Zikova
• Lectures: Wednesdays 12:00 a.m.
• Practice: Wednesday ~2:00 p.m. Required: cesnet/metacenter/elixir mediated VM, laptop
• Consultation: Wednesday mornings or Thursday afternoon at VŠCHT, room B1314. Or by email.
• http://bio.img.cas.cz/GAA2024

Syllabus (indicative)

• sequencing experimental methods
• data formats used in bioinformatics
• bioinformatics databases and other Internet resources
• genome browsers
• motif search
• alignment
• advanced alignment methods (PSI-Blast, HMMER, profiles)
• multiple alignment
• genome assembly (de novo, mapping)
• gene prediction
• annotation of genomic data
• methods using second generation sequencing (ht-seq assays: RNA-Seq, Chip-Seq, C3-based, Epigenomics)
• RNA 2D structure - RNA folding

Seminar work

Links

• Lectures are on VM in the Lectures directory
• GAA script (in czech)
• Exercises