Madison, United States (16th June 2010)

Working with Zebrafish Genome Resources

Capitol Ballroom A, The Madison Concourse Hotel, Madison, WI, USA
Ref: ODW-Madison

APPLICATIONS NOW CLOSED

Course Summary

In association with the 9th International Meeting on Zebrafish Development and Genetics and the Wellcome Trust Sanger Institute, we are pleased to announce a one day "Working with Zebrafish Genome Resources" Workshop (The workshop will run from 09:00 - 16:30).

Each participant will be required to provide their own wireless enabled laptop for the duration of the course.

Each workshop is broken into modules designed to give a broad overview of a given topic with examples chosen by the trainers. The modular structure consists of a discussion of theory and methods, coverage of software and web resources, and a series of "hands on" worked examples. Time is provided in each session for participants to carry out their own research in the presence of the trainers, and participants are encouraged to bring their own problems (e.g sequence for analysis) with them. All materials used during the workshop series will be available on the Web, in the form of manuals and information. Zebrafish specific examples will be used wherever possible.

This course is limited to 40 participants and will be held in English.

The course manual will be made available as a PDF and will be sent out to participants one week prior to the course, and will also be available online during the workshop.

Please visit the application page for further details and on-line registration or expression of interest in future workshops.

There will be a course fee of $50 for all participants. Participants will be expected to arrange and fund their own travel and accommodation.

Topics

Databases and de novo analysis of sequence

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

Genome Browsing

  • Ensembl - full coverage including BioMart
  • VEGA
  • UCSC

Exploring Sequence Variation and Disease:

  • Understanding Protein Function - from domains to structure (covering Pfam, InterPro, TreeFam CDD, CATH, SCOP, PDB, MSD)
  • Disease databases COSMIC, OMIM, DECIPHER
  • Mapping disease associated SNPs to Proteins - Polyphen, SNPs
  • Ensembl SNP information, Geneview in dbSNP
  • 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

Timetable

Preliminary Timetable

  • 09:15 - 09:30 Introduction
  • 09:30 - 10:45 Databases and de novo analysis of sequence
  • 10:45 - 11:00 Coffee break
  • 11:00 - 12:45 Genome browsing
  • 12:45 - 13:30 Lunch
  • 13:30 - 15:00 Exploring sequence variation and disease
  • 15:00 - 15:15 Coffee break
  • 15:15 - 16:30 Comparative sequence analysis

Contact

The Open Door Workshops were conceived jointly by The Sanger Institute and the Cold Spring Harbor Laboratories, and are being developed further by staff at these centres with assistance from staff at the Wellcome Trust and the University of Cambridge.

Queries

Any queries should be sent to zebrafish-odw@sanger.ac.uk

Deadlines

  • Notification of places will be given one week after receipt of successful application.
  • Full payment will be required within five working days of notification of a place.
* quick link - http://q.sanger.ac.uk/p002y9m8