1. 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.

2. 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

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

4. Retrieve FASTA sequence Slides last updated May 2009 4 FASTA

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

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10. 10 Slides last updated May 2009

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

13. The BLAST hit list Slides last updated May 2009 13

14. BLAST local pairwise alignment 14 Slides last updated May 2009

15. 15 Distance tree of results

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

17. 17 Taxonomy reports

18. 18 Sorting BLAST results by Taxonomy Slides last updated May 2009

19. 19 Formatting options

20. 20 Limit Results by Organism Slides last updated May 2009

21. Links NCBI BLAST page http://www.ncbi.nlm.nih.gov/BLAST/ The NCBI Query Tutorial http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/quer y_tutorial.html The NCBI BLAST Tutorial http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/tut1.html The NCBI BLAST Program Selection Guide. http://www.ncbi.nlm.nih.gov/blast/producttable.shtml 21 Slides last updated May 2009