VCU Bioinformatics and Bioengineering Summer Institute
Virginia Commonwealth University
imageimageHomeBio What?The InstituteThe People
The Institute
Goals of the Institute
Two-year Plan
Course web pages
News
Archives
Application process
About the BBSI

Research Simulation
The origin of human genetic variability from
cross-species comparisons: The truth about Blast
The Workings of Blast

Time: Tuesday, June 29, 9:00 am - noon
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizer: Jeff Elhai
Audience: Primarily 1st year students

Topics of session

  • Discussion of Smith-Waterman algorithm
  • Exercise: Fill out Smith-Waterman scoring table
  • Use of BlastN.pl to understand how Blast works

Resources of session

  • Notes: Alignment of DNA sequences
  • Program: BlastN.pl - A homegrown version that runs Blast over nucleotide sequences, for your inspection and testing
  • Data: DG47.nt - a file used by BlastN as a query sequence
  • Data: lef.nt - a file used by BlastN as a subject sequence
  • Data: chimp-rs1140646-region.fa - 100 nt of sequence sent by colleague containing sequence supposedly matching rs1140646

Before coming to the session