Exploring Biological Sequences

Date:

 Tuesday 8 Thursday 10 October 2019

Venue: 

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

Application opens: 

Monday 08 April 2019

Application deadline: 

Friday 13 September 2019

Participation: 

First come, first served

Contact: 

Meredith Willmott

Registration fee: 

£130

Registration closed

Find other similar courses »

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
  • Using sequences to investigate families, function and structure

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 and programmatic access interfaces
  • Tools for sequence searching and alignment:
    • FASTA, BLAST, PSI-SEARCH, HMMER
    • Clustal Omega, MUSCLE
  • ENA and UniProt sequence databases
  • Ensembl Genome Browser
  • InterPro and PDBe resources

 

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
  • Perform further analyses on sequences to help examine their possible functions

Programme

Day 1 – Tuesday 08 October 2019
08:30 Shuttle from Cambridge Station (Stop 5)  
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 ENA nucelotide database Sam Holt
11:30-12:30 Introduction to sequence searching Fabio Madeira & Nandana Madhusoodanan
12:30-13:00 Lunch  
13:00-15:00 Introduction to sequence searching Fabio Madeira & Nandana Madhusoodanan
15:15-15:30 Break  
15:30-16:00 Modelling protein evolution and variation using structural information Umberto Peron
16:30-16:30 Short-range template switching in the human genome Conor Walker
16:30-17:00 Discussion  
17:00 End of day  
17:15 Shuttle to Cambridge Station (Stop 5)  
Day 2 – Wednesday 09 October 2019
08:30 Shuttle from Cambridge Station (Stop 5)  
09:00-09:15 Arrival and registration  
09:15-10:45 Multiple sequence alignments Fabio Madeira & Nandana Madhusoodanan
10:45-11:00 Break  
11:00-12:30 Multiple sequence alignments Fabio Madeira & Nandana Madhusoodanan
12:30-13:00 Lunch  
13:00-14:00 Programmatic access at EMBL-EBI Fabio Madeira & Nandana Madhusoodanan
14:00-15:00 Exploring genomes in Ensembl Ben Moore
15:00-15:15 Break  
15:15-17:00 Exploring genomes in Ensembl Ben Moore
17:00 End of day  
17:15 Shuttle to Cambridge Station (Stop 5)  
Day 3 – Thursday 10 October 2019
08:30 Shuttle from Cambridge Station (Stop 5)  
09:00-09:15 Arrival and registration  
09:15-10:45 Exploring protein sequences in UniProt Rossana Zaru & Hema Bye-A-Jee
10:45-11:00 Break  
11:00-12:30 Exploring protein sequences in UniProt Rossana Zaru & Hema Bye-A-Jee
12:30-13:00 Lunch  
13:00-14:30 Using predictive models to understand protein families, domains and function Lorna Richardson
14:30-15:30 From sequence to structure David Armstrong
15:30-15:45 Break & group photo   
15:45-16:45 From sequence to structure David Armstrong
16:45-17:00 Wrap-up and feedback Tom Hancocks
17:00 End of workshop  
17:15 Shuttle to Cambridge Station (Stop 5)