Genomics: analysis and algorithms

Jan Pačes

News and changes.

• There is no lecture on September 17th.

Who, when, where

• Lecturer: Jan Pačes; Email: hpaces@img.cas.cz; Subject: GAA
• 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/GAA2026

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