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Mon 11 May - Wed 13 May 2015
09:30, ...

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview
BeginnersPrerequisites

Mon 11 May - Wed 13 May 2015

Description

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.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here
  • Further details regarding the charging policy are available here
Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Mon 11 May 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map James Procter,  Geoff Barton,  Suzanne Duce
2 Tue 12 May 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map James Procter,  Geoff Barton,  Suzanne Duce
3 Wed 13 May 2015   09:00 - 16:00 09:00 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Geoff Barton,  James Procter,  Suzanne Duce
Format

Presentations, demonstrations and practicals

Duration

3

Frequency

Once per year

Theme
Specialized Training

Booking / availability