Course at EMBL-EBI
Exploring biological sequences
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.
Who is this course for?
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.
What will I learn?
Learning 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
Course content
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
Trainers
Tom Hancocks
EMBL-EBI, UK Sam Holt
EMBL-EBI, UK Fabio Madeira
EMBL-EBI, UK Nandana Madhusoodanan
EMBL-EBI, UK Umberto Perron
EMBL-EBI, UK Conor Walker
EMBL-EBI, UK Rossana Zaru
EMBL-EBI, UK Hema Bye-A-Jee
EMBL-EBI, UK Lorna Richardson
EMBL-EBI, UK David Armstrong
EMBL-EBI, UK Benjamin Moore
EMBL-EBI, UK
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)
Attendance at this workshop is allocated on a first come, first served basis.
The registration fee covers your lunch, refreshments and a shuttle between Station Road, Cambridge and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.
Please note that registration closes two weeks prior to the course, so please register as soon as you can. Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
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) |
Attendance at this workshop is allocated on a first come, first served basis.
The registration fee covers your lunch, refreshments and a shuttle between Station Road, Cambridge and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.
Please note that registration closes two weeks prior to the course, so please register as soon as you can. Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.