Searching for sequences: introduction to databases and sequence analysis tools - August 2014

Section outline

• Select section General

  General

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  Searching for sequences: introduction to databases and sequence analysis tools

  Fribourg, 28 August 2014

  Overview

  This one day workshop will cover the practical use of sequence databases and tools to discover and extract DNA and protein sequences.
  Participants will learn more about NCBI RefSeq, ENA, SRA, UniProtKB, ENSEMBL, Blast, ExPASy, etc...
  
  

  Requirements

  Skills requirements: none

  Material requirements: The course will consist of theory and practical exercises. Participants should bring their own laptops with at least 4Gb RAM and WIFI capable.
  
  

  Application

  Application is closed. The course is full.
  Please note that the participation to this workshop costs Frs 50.- to cover material and coffee breaks. Participants from non-academic institutions should contact us.

  Deadline for registration and cancellation is set to the 15th of August 2014.
  

  Location

  • Université de Fribourg

  • Building Pérolles PER21, room C130

  You can reach it (stop "Charmettes") by bus Nr 1, 3 or 7 from the train station (5min) or by walking (15min).
  
  

  Additional information

  The course will be taught by Dr Laurent Falquet.

  No exam planned.

  You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

  For more information, please contact training@isb-sib.ch
• Select section Topic 1

  Topic 1

  Not available
• Select section Schedule Part 1

  Schedule Part 1

  9:15 Welcome

  9:30 Quick introduction to public databases (DNA and Proteins)

  10:00 Practical 1: Sequence searching with keywords

  10:30 Coffee break

  • Select activity Practical 1A NCBI

    

    Practical 1A NCBI Page
  • Select activity Practical 1B UniProtKB

    

    Practical 1B UniProtKB Page
• Select section Part 2

  Part 2

  11:00 Sequence searching with other sequences

  11:30 Practical 2: BLAST and BLAT, PSI-BLAST

  12:30 Lunch break

  • Select activity Practical 2 BLAST/BLAT

    

    Practical 2 BLAST/BLAT Page
• Select section Part 3

  Part 3

  13:30 Genome Browsers (ENSEMBL, UCSC) and their tools

  14:00 Practical 3: Sequence searching with BioMart

  15:00 Coffee break

  • Select activity Practical 3 ENSEMBL/BIOMART

    

    Practical 3 ENSEMBL/BIOMART Page
• Select section Part 4

  Part 4

  15:30 Users own problems in sequence searching

  17:00 Farewell