RNA12
RNA BioinformaticsCourse 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 Last updated: May 10th 2012 |