Johannesburg, South Africa (Thursday 10th - Saturday 12th October 2013)

Working with the Human Genome Sequence

The Maslow Hotel, Sandton, Johannesburg
Ref: ODW-Johannesburg

APPLICATIONS NOW CLOSED

Course Summary

The workshop is being held at The Maslow Hotel, Sandton, Johannesburg, as a post-meeting event to the Southern African Society for Human Genetics (SASHG) 2013 Congress. This three-day workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned.

This course is limited to 30 participants and is free to attend for non-commercial applicants. Teaching materials, lunch and refreshments will be provided. Participants will need to make their own travel and accommodation arrangements and bring a laptop computer to use for the duration of the course.

Course instructors

  • Matthew Clark (The Genome Analysis Centre)
  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Robert Finn (Janelia Farm Research Campus)
  • Charles Steward (Welcome Trust Sanger Institute)
  • Emily Pritchard (EBI)
  • Matt Forrest (TwistDX)

How to apply

  • Pre-requisites - The workshops are aimed at research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff as well as specialists in related fields. Acceptance will be subject to selection process.
  • Cost - There will be no course fee for academics. The course fee for commercial applicants is £1000.
  • Applications - Applicants will be required to complete an online application form together with a 250-word outline of the relevance of the course to their work. Please note that documentation supporting the application will be required from the applicant's Supervisor/Head of Department.

Queries

Any queries should be sent to opendoor@sanger.ac.uk.

Deadlines

  • Closing date for application is 13th September 2013. Applications will not be accepted after this date.
  • Notification of places will be as soon as possible after the closing date.
  • Full payment (if required) due on TBA.

Sequence Formats and Retrieval:

  • DNA databases: Embl, Genbank, DDBJT
  • Protein databases: Uniprot
  • Entrez - seach sequence information, including Refseq
  • BLAST

Genome Browsing:

  • Ensembl - full coverage including BioMart
  • VEGA
  • UCSC

de novo analysis of Sequence:

  • VEGA
  • DNA analysis - ORF finder
  • Alignment of splicing cDNA to genomic DNA - Spidey, Est2genome, SIM4
  • Multiple Sequence Alignment - CLUSTALW
  • Alignment viewing and Editing- Jalview, GeneDoc

Exploring Function and Disease:

  • Understanding Protein Function - from domains to structure (covering Pfam, InterPro, TreeFam CDD, CATH, SCOP, PDB, MSD)
  • Proteins as part of functional networks - iPfam, IntAct
  • Secondary Structure predictions
  • Disease databases COSMIC, OMIM, DECIPHER
  • Mapping disease associated SNPs to Proteins - Polyphen, SNPs 3D Rfam and microRNAs (miRBase)

Sequence Variation:

  • Ensembl SNP information, Geneview in dbSNP
  • Glovar, JSNP, HGVBase
  • Genotyping
  • Haplotypes and HapMap
  • Haploview

Comparative Sequence Analysis:

  • Homologous gene identification - Paralogues and Orthologues
  • Ensembl - orthologue prediction, MultiContigView
  • EntrezGene - BLink, Homologene
  • Comparative Genome Analysis - UCSC, Zpicture, VISTA

Day one

  • 09:00 - 09:30 Registration and coffee
  • 09:30 - 10:30 Introduction/participant talks
  • 10:30 - 11:00 Coffee
  • 11:00 - 13:00 Module 1 (sequence formats and retrieval)
  • 13:00 - 14:00 Lunch
  • 14:00 - 16:00 Module 2 (de novo analysis of sequence)
  • 16:00 - 16:30 Tea
  • 16:30 - 17:30 Own research

Day two

  • 09:00 - 11:00 Module 3 (Ensembl)
  • 11:00 - 11:30 Coffee
  • 11:30 - 12:30 Module 3 continued
  • 12:30 - 13:30 Lunch
  • 13:30 - 14:30 Own research
  • 14:30 - 16:30 Module 4 (Comparative)
  • 16:30 - 17:00 Coffee
  • 17:00 - 18:00 Tasks and own research

Day three

  • 09:00 - 11:00 Module 5 (Protein and expression)
  • 11:00 - 11:30 Coffee
  • 11:30 - 13:30 Module 6 (Variation)
  • 13:30 - 14:30 Lunch
  • 14:30 - 15:30 mop-up session
  • 15:30 - 16:00 Coffee/end of workshop
* quick link - http://q.sanger.ac.uk/el94q64h