Exploring Biological Sequences

Date:

 Tuesday 13 Thursday 15 November 2018

Venue: 

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

Application opens: 

Monday June 04 2018

Application deadline: 

Friday October 05 2018

Participation: 

First come, first served

Registration fee: 

£130.00

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 searching for, accessing and aligning sequences; through the use of sample datasets participants will learn how to discover more about the biological context of nucleotide and 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

This course is currently under development and full details about the course are not yet available. If you would like to be informed when applications open for this course then please click on the “Register your interest” button above.

If you would like to see details of similar course from previous years, please take a look at our course listings, using the filter boxes to refine your search by year and subject.

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, EMBL-EBI web services

Outcomes

After this course you should be able to: (There should only be 4-6 objectives)

  • 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

Day 1 – Tuesday 13 November 2018

08:30 Coach from Cambridge Station  
09:00-09:15 Arrival and registration  
09:15-09:30 Welcome and introduction to the 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 Sam Holt
11:30-12:30 UniProt protein database Rossana Zaru & Hema Bye-A-Jee
12:30-13:00 Lunch  
13:30-15:00 Introduction to sequence searching Andrew Cowley
15:00-15:15 Break  
15:15-17:00 Sequencing searching and alignments Andrew Cowley
17:00 End of day  
17:15 Coach to Cambridge Station  

Day 2 – Wednesday 14 November 2018

08:30 Coach from Cambridge Station  
09:15-10:45 Fast, sensitive homology detection using HMMER HMMER Team
10:45-11:00 Break  
11:00-12:30 Multiple sequence alignments Andrew Cowley
12:30-13:00 Lunch  
13:00-14:30 Multiple sequence alignments Andrew Cowley
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  
17:15 Coach to Cambridge Station  

Day 3 – Thursday 15 November 2018

08:30 Coach from Cambridge Station  
09:15-10:45 Exploring protein sequences Rossana Zaru & Hema Bye-A-Jee
10:45-11:00 Break  
11:00-12:30 Understanding families, domains 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  
16:45-17:00 Wrap-up and feedback Tom Hancocks
17:00 End of workshop  
17:15 Coach to Cambridge Station