From sequence to gene: genome resources at the EBI

Date:

  Wednesday 5 March 2008

Contact: 

Alison Barker

Registration closed

Overview

This course will provide you with an overview of various nucleotide sequence and genome resources at the EBI.

As part of the course a presentation will be given by a member of the HAVANA team of the Wellcome Trust Sanger Institute, focusing on how they manually annotate genomes and what problems they encounter in the process of doing this.

Topics include

  • retrieving nucleotide sequences using EMBL-Bank
  • analysing nucleotide sequences using EMBOSS
  • browsing annotated genomes using Integr8, Genome Reviews and Ensembl
  • datamining annotated genomes using BioMart
  • searching across all EBI resources using EB-eye
  • doing literature searches using CiteXplore and EBI text mining tools

Additional information

Course materials are available to download from the following link:

/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2008/course_080305_genes.zip

Programme

Time Topic Trainer/Speaker
Day 1  
12:30 - 13:30 Lunch and Registration
13:30 - 13:45 Introduction Bert Overduin
13:45 - 14:00 Searching across all EBI resources using EB-eye Bert Overduin
14:00 - 15:00 Overview of EMBL-Bank Bob Vaughan
15:00 - 15:15 Tea
15:15 - 17:15 Analysing nucleotide sequences using EMBOSS Peter Rice
Day 2  
09:30 - 10:30 Browsing annotated genomes using Integr8 and Genome Reviews Paul Kersey
10:30 - 10:45 Coffee
10:45 - 12:15 Browsing annotated genomes using Integr8 and Genome Reviews Paul Kersey
12:15 - 13:15 Lunch
13:15 - 15:15 Browsing annotated genomes using Ensembl Bert Overduin
15:15 - 15:30 Tea
15:30 - 17:15 Browsing annotated genomes using Ensembl Bert Overduin
Day 3  
09:30 - 10:30 Lecture: Manual annotation of vertebrate genomes Jane Loveland
10:30 - 10:45 Coffee
10:45 - 12:30 Datamining annotated genomes using BioMart
Giulietta Spudich