RNA12

RNA Bioinformatics

Course Timetable (provisional)
Tue, May 15th Introduction to RNA, RNA structure prediction, RNA homology search
Day #1
09:30 - 11:00 Introduction to RNA
-Why is RNA interesting
-Primary, secondary and tertiary structure

11:00 - 11:30 Coffee Break
11:30 - 12:30 RNA structure prediction
-single sequence methods (MFE, Boltzmann, sampling)
12:30 - 14:00 Lunch Break
14:00 - 16:00 RNA structure prediction
-comparative (Alignment folding, Sankoff, meta-methods)
RNA homology search
-single sequence (BLAST, FASTA)
-profile methods (HMMs, CMs/SCFGs)
16:00 - 16:30 Tea Break
16:30 - 18:00 RNA homology search
-specialised methods eg. tRNAscan-SE and RNAMMER
-Rfam
Wed, May 16th Predicting ncRNA, RNAi: miRNA & siRNA
Day #2
09:30 - 11:00 Predicting ncRNA
-QRNA, RNAz, EvoFold
11:00 - 11:30 Coffee Break
11:30 - 12:30 Predicting ncRNA
-RNA-seq
12:30 - 14:00 Lunch Break
14:00 - 16:00 small non-coding RNAs
-introduction to siRNAs, microRNAs and piRNAs
- miRBase and miRBase Genomic Analysis
- prediction of microRNAs with MapMi
16:00 - 16:30 Tea Break
16:30 - 18:00 microRNA and siRNA target prediction
- Target prediction, approaches and problems
- de novo prediction using TargetScan and Microcosm
- combining experiment and prediction for siRNA and miRNA analysis
Thu, May 17th Next generation sequencing, Specific examples
Day #3
09:30 - 11:00 New technology sequencing for small RNAs
- Next-Gen sequencing approaches and problems
- Profiling small RNAs using next-gen sequencing
- Mapping sequence to the genome
- Practical session with a FASTQ file from microRNA profiling sequence run
11:00 - 11:30 Coffee Break
11:30 - 12:30 Specific examples:
-miRNAtools: a web repository of tools for miRNA analysis
-Switches: riboswitches, thermosensors, pH-sensor
12:30 - 14:00 Lunch Break
14:00 - 16:00 Specific examples:
-snoRNAs: inside-out genes (GAS5), orphan snos, PWS, splicing regulation...
-6S RNA, Y RNA
-Dual function snoRNAs eg. sno-mi-RNAs, SgrS, RNAIII, SRA, VegT, Oskar, enod40.
16:00 - 16:30 Tea Break
16:30 - 18:00 Final considerations, course wrap-up
Course Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:   May 10th 2012