RNA Bioinformatics
In this seminar, some typical questions of RNA bioinformatics will be approached.
[ course wiki ]
[ download tasks and material for day 3 ]
[ download abstracts from day 1 ]
Problem 1: How does an RNA sequence fold?
You know the sequence, but want to know the secondary structure.
[ download example RNA sequences A ]
[ download example RNA sequences B ]
[ download example RNA sequences C ]
[ download example RNA sequences D ]
[ download example RNA sequences E ]
[ download example RNA sequences F ]
Problem 2: What does a set of RNAs have in common?
You have a set of RNA sequences, and want to know whether they have common features.
[ download example RNA sequences A ]
[ download example RNA sequences B ]
Problem 3: Is a protein DNA/RNA-binding?
You have a protein sequence, but want to know whether it can bind DNA or RNA.
[ download example protein sequences A ]
Problem 4: What are possible 3D structures for a given sequence?
You know the sequence, but want to get an idea how the 3D structure could look like.
[ download example RNA sequence A ]
[ download example RNA sequence B ]
Problem 5: What motifs can be found in a 3D structure?
If you know the 3D structure of a RNA already, what can you tell from it?
[ download example RNA structure A ]
[ download example RNA structure B ]
Problem 6: Similarity search in a known set of sequences
If you have a sequence that you want to compare to a custom set of other sequences, how do you do that?
[ set of sequences with three example queries ]
Problem 7: Identifying miRNA sequences
How to distinguis miRNA transcripts from other sequences. The example contains 5 miRNAs and 5 other sequences.
[ download example sequences ]
Schedule
| date | time | room | topic |
|---|---|---|---|
| Nov 23rd | 9.30 | 1.126 | Introduction |
| Nov 30th | 9.30 | 1.126 | miRNAs and BLAST |
| Dec 7th | 9.30 | 1.126 | to be announced |
| Jan ?? | 9.30 | 1.126 | to be announced |
| Jan ?? | 9.30 | 1.126 | to be announced |