Exploring Biological Sequences

Date:

 Tuesday 14 Thursday 16 November 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday June 05 2017

Application deadline: 

Friday October 06 2017

Participation: 

First come, first served

Contact: 

Charlotte Pearton

Registration fee: 

£120

Registration closed

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Overview

This workshop will introduce basic bioinformatics approaches that are used to find, analyse and understand nucleotide or protein sequences. It will explore how to conduct searches across biological databases using both metadata and sequence data approaches. The course will explain how sequence searching techniques work, and how to use them effectively to find relevant results. Practical exercises will develop skills in locating and aligning sequences, and provide guidance on how to learn more about the biological context of nucleotide or protein sequences.

The key areas covered by the workshop will include:

  • Sequence data resources at EMBL-EBI
  • Tools for sequence searching and alignments
  • Methods for conducting phylogenetic analysis
  • Using sequences to investigate families, function and structure

Audience

The course is aimed at researchers interested in core bioinformatics techniques, sequence searching and alignment. No prior experience of bioinformatics is required, but familiarity with biological databases and web tools would help. An undergraduate level understanding of molecular biology would be of benefit to those attending the workshop.

Syllabus, tools and resources

During this course you will learn about:

  • EBI Search interface, ENA and UniProt databases
  • Sequence searching tools – FASTA, BLAST, PSI-SEARCH, HMMER
  • Multiple sequence alignment tools – Clustal Omega, MUSCLE
  • Phylogeny tools
  • InterPro, PDBe, Ensembl VEP

Outcomes

After this course you should be able to:

  • Understand basic methods for bioinformatics data searching
  • Find relevant database entries using sequence searching methods
  • Conduct alignments of multiple sequences via a variety of methods
  • Construct basic phylogenetic trees
  • Perform further analyses on sequences to help examine their possible functions

Programme

Time Topic Trainer
Day 1 - Introducing and searching database
09:15 - 09:30 Welcome and introduction to workshop Tom Hancocks
09:30 - 10:30 Searching for data at EMBL-EBI Tom Hancocks
10:30 - 10:45 Break  
10:45 - 11:30 European Nucleotide Archive Nicole Silvester
11:30 - 12:30 UniProt protein database Rossana Zaru & Klemens Pichler
12:30 - 13:00 Lunch  
13:00 - 15:00 Introduction to sequence searching Tom Hancocks
15:00 - 15:15 Break  
15:15 - 17:00 Sequence searching and alignments Tom Hancocks
17:00 End of day  
Day 2 - Exploring sequence alignments and evolutionary relationships
09:15 - 10:45 Fast, sensitive homology detection using HMMER Rob Finn
10:45 - 11:00 Break  
11:00 - 12:30 Multiple sequence alignments Tom Hancocks
12:30 - 13:00 Lunch  
13:00 - 14:30  Multiple sequence alignments Tom Hancocks
14:30 - 15:15 Introduction to phylogenies Birgit Meldal
15:15 - 15:30 Break  
15:30 - 17:00 Constructing phylogenies Birgit Meldal
17:00  End of day  
Day 3 - Beyond sequence: bringing functional annotation to the table
09:15 - 10:45 Exploring protein sequences

Rossana Zaru & Klemens Pichler

10:45 - 11:00 Break  
11:00 - 12:30 Understanding families, domins and function  Lorna Richardson
12:30 - 13:00 Lunch   
13:00 - 15:30 From sequence to structure David Armstrong
15:30 - 15:45 Break  
15:45 - 16:45 Programmatic access to EMBL-EBI Anna Foix & Joon Lee
16:45 - 17:00 Wrap up and feedback Tom Hancocks
17:00