Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview
Organizer: University of Cambridge
Host institution: University of Cambridge Bioinformatics Training
Start: Monday, 11 May 2015 @ 08:30
End: Wednesday, 13 May 2015 @ 15:00
Venue: Craik-Marshall Building
Country: United Kingdom
Postcode: CB2 3ARTarget audience:
- Graduate students
- Postdocs and Staff members from the University of Cambridge
- Institutions and other external Institutions or individuals
Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA.
Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication.
The course involves of a mixture of talks and hands-on exercises.
Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview.
Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch.
Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues.
There will be opportunities for attendees to get advice on analysis of their own sequence families.
Further information, including some training videos, is also available.
- Workshops and courses