MICB 405 Bioinformatics MiniLab 2 BLAST Dr Joanne

MICB 405 Bioinformatics Mini-Lab #2 - BLAST Dr. Joanne Fox joanne@msl. ubc. ca We gratefully acknowledge the funding for the development of these teaching materials provided by UBC students through the Teaching and Learning Enhancement Fund (TLEF) from 2005 -2007.

Objectives • By the end of today’s tutorial: – You will use the web interface at the NCBI to run a BLAST search. – You will investigate the graphical view, the BLAST “hits” list, and the pairwise alignments for the results of this BLAST search. – You will view the taxonomy reports for this BLAST result. Slides last updated May 2009 2

Search Entrez for NP_644805. 1 search Slides last updated May 2009 3

Retrieve FASTA sequence FASTA Slides last updated May 2009 4

Copy (and Paste) Sequence Slides last updated May 2009 5

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A graphical view of your BLAST results: Slides last updated May 2009 12

The BLAST hit list Slides last updated May 2009 13

BLAST local pairwise alignment Slides last updated May 2009 14

Distance tree of results Slides last updated May 2009 15

BLAST Tree View Widget Stat 5 A Stat 5 B Slides last updated May 2009 16

Taxonomy reports Slides last updated May 2009 17

Sorting BLAST results by Taxonomy Slides last updated May 2009 18

Formatting options Slides last updated May 2009 19

Limit Results by Organism Slides last updated May 2009 20

Links • NCBI BLAST page http: //www. ncbi. nlm. nih. gov/BLAST/ • The NCBI Query Tutorial http: //www. ncbi. nlm. nih. gov/Education/BLASTinfo/que ry_tutorial. html • The NCBI BLAST Tutorial http: //www. ncbi. nlm. nih. gov/Education/BLASTinfo/tut 1. html • The NCBI BLAST Program Selection Guide. http: //www. ncbi. nlm. nih. gov/blast/producttable. shtml Slides last updated May 2009 21