300599 UE Praktikum Bioinformatik

3 stündiges Blockpraktikum. Ziel ist die selbstständige Durchführung eines kleinen bioinformatischen Forschungsprojekts

Ort: Computer-Praktikumsraum des Inst. f. Theoret. Chemie,
Rennweg 95b, 1030 Wien EINGANG: Dr. Bohrg. 7, großes Gebäude im Hof.

Thema 2010/11:
Genannotation durch Promotorsuche

Background

Protein coding genes are usually identified on the basis of the codon bias characteristic for ORFs. An alternative that does not rely on features of coding sequences is to search for the promotor sequences of the transcript. in this course we will concentrate on Pol III transcripts which feature especially distinct promotor motifs.

One difficulty of the approach is that promotor motifs tend to vary considerably from species to species. It is therefore necessary to identify promotor motifs in each species (or at least for different phylogenetic subgroups) by inspecting the upstream regions of known Pol III genes such as U6 snRNAs etc.

Introductory Slides

RNAs know to be Pol III transcripts with external promoters

Literature

Literature search at: http://www.ncbi.nlm.nih.gov/pubmed/

Data bases

Ensembl http://www.ensembl.org/index.html
UCSC Genome browser http://genome.ucsc.edu/
BLAST @ NCBI http://blast.ncbi.nlm.nih.gov/Blast.cgi

Programs

Jalview - multiple alignment editor http://www.jalview.org
Seaview - multiple alignment editor http://pbil.univ-lyon1.fr/software/seaview.html