Course overview
In this course participants will explore EMBL-EBI resources for genomics and sequence alignments. The sessions focus on sequence similarity searching and alignments as well as accessing, retrieving genomic data for a variety of organisms from Ensembl/Ensembl genome browser.
The course will be delivered by experienced and dedicated EMBL-EBI trainers, and will involve presentations, demonstrations and practical exercises to give participants hands on experience.
Audience
The course is aimed at researchers in the Romanian bioinformatics and biological research community who have minimum or no prior experience in bioinformatics and/or are interested in exploring and using EMBL-EBI resources for their research. No knowledge of programming is required, but an undergraduate level knowledge of biology and/or biochemistry would be beneficial.
Modules and Resources
During this course you will learn about:
* An overview of EMBL-EBI resources
* Sequence searching and Alignment
* Ensembl genome browser
Learning Objectives
After this course you should be able to:
* Describe the principles of sequence similarity searching and sequence homology
* Use the different sequence similarity searching tools to find homologous sequences at EMBL-EBI and identify the appropriate tool for different applications
* Carry out appropriate pairwise and multiple sequence alignments using the tools available at EMBL-EBI and combine different techniques in an analysis workflow
* View genomic regions and manipulate the view to add features you are interested in.
* Analyse genomic variants and associated phenotypes and your own variation data using the VEP.
* View homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.
A detailed description below.
1) Introduction to EBI resources and tools
2) Sequence search and alignment
Overall: Understand and use tools like BLAST, PSI-SEARCH and Clustal Omega to find and align homologous sequences at EMBL-EBI
Description This module covers sequence similarity searching and alignment, using tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, and pairwise and multiple sequence alignment tools like Clustal Omega to discover conserved regions of sequences and sequence relationships. It includes tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages.
The module is aimed at researchers interested in core bioinformatics techniques, sequence searching and alignment. No prior experience of bioinformatics is required, but an undergraduate level knowledge of molecular biology would be of benefit to
those attending.
Resources
* Sequence searching tools – BLAST, FASTA, PSI-BLAST, PSI-SEARCH, HMMER
* Pairwise alignment tools – EMBOSS water, needle
* Multiple sequence alignment tools – Clustal Omega, MUSCLE.
Learning outcomes
Participants should be able to:
= describe the principles of sequence similarity searching and sequence homology
= use the different sequence similarity searching tools to find homologous sequences at EMBL-EBI and identify the appropriate tool for different applications
= carry out appropriate pairwise and multiple sequence alignments using the tools available at EMBL-EBI
= combine different techniques in an analysis workflow
Course Structure
This course is mixed format, with lectures and demonstrations interspersed with practical exercises.
3) Ensembl Genomes
Description This interactive module offers participants hands-on experience in the use of the Ensembl and/or Ensembl Genomes genome browsers. Ensembl provides access to the human, mouse, zebrafish and other (mostly vertebrate) genomes, whilst Ensembl Genomes focuses on bacteria, protists, fungi, plants and invertebrate metazoa. We will customise the module to cover a selection of the following topics depending on your interests. This module can be tailored for species of interest (choosing Ensembl and/or Ensembl Genomes as appropriate), new or frequent users from the wet-lab, or bioinformaticians.
Resources
Ensembl and Ensembl genomes
Learning outcomes
Participants should be able to:
* view genomic regions and manipulate the view to add features you are interested in.
* explore information about genes and their sequences, and gene data in bulk using BioMart.
* analyse genomic variants and associated phenotypes and your own variation data using the VEP.
* view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.
Format
The course will consist of six short sessions, each with a presentation, a demo and some exercises:
* Looking at species and regions
* Genes and transcripts
* Variation and VEP
* Gene regulation
* Comparative genomics
* BioMart
4) IntAct webinar (24 April, 11:30 am GMT+2)
This webinar will cover IntAct and some aspects of the Complex Portal
One Comment