Introduction to Computational RNA Biology (Cambridge, UK)
This course will give an overview of RNA and the informatic challenges associated with studying RNA. It will be run as a mixture of lectures and hands-on problem solving sessions.
Objectives
This course is practical in nature. We will introduce RNA secondary structure prediction, state of the art RNA homology search tools, methods for predicting RNA:RNA interactions, and comparative methods for studying RNA sequence and structure. After participating attendees will be able to use current methods and be aware of limitations in RNA informatics. In addition we will cover recent advances in high-throughput methods for discovering and characterizing small RNAs, including Piwi-interacting RNAs and microRNAs. This will include an introduction to processing size-selected RNA-seq data, microRNA target prediction using microarrays and Sylamer, and CLIP-Seq.
Course Pre-requisites:
Basic Molecular Biology. Graduate level understanding of Molecular Biology. A basic level of computer knowledge will be assumed.
Target Audience:
Biologists interested in applying computational tools for RNA sequence analysis to their research.
| Day One | Introduction to RNA, RNA structure prediction, RNA homology search |
| 09:30 - 11:00 | - Introduction to RNA - Why is RNA interesting? - Primary, secondary and tertiary structure |
| 11:00 - 11:20 | Coffee Break |
| 11:20 - 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 - 16:20 | Tea Break |
| 16:20 - 17:30 | - RNA homology search - Specialised methods eg. tRNAscan-SE and RNAMMER - Rfam |
| Day Two | Predicting ncRNA, RNAi: miRNA & siRNA foo |
| 09:30 - 11:00 | - Predicting ncRNA - QRNA, RNAz, EvoFold |
| 11:00 - 11:20 | Coffee Break |
| 11:20 - 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 - 16:20 | Tea Break |
| 16:20 - 17:30 | - 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 |
| Day Three | Next generation sequencing, Specific examples foo |
| 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 - 11:20 | Coffee Break |
| 11:20 - 12:30 | - Specific examples: - miRNAtools: a web repository of tools for miRNA analysis (miRNAtools website) - 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 - 16:20 | Tea Break |
| 16:20 - 17:30 | Final considerations, course wrap-up |
Additional Resources:
Details can be found here: http://training.csx.cam.ac.uk/event/606100