MICB 405 BioinformaticsMini-Lab #2 - BLAST

Dr. Joanne Foxjoanne@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.

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Search Entrez for NP_644805.1

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search

Retrieve FASTA sequence

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FASTA

Copy (and Paste) Sequence

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A graphical view of your BLAST results:

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The BLAST hit list

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BLAST local pairwise alignment

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Distance tree of results

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BLAST Tree View Widget

Stat 5A

Stat 5B

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Taxonomy reports

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Sorting BLAST results by Taxonomy

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Formatting options

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Limit Results by Organism

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Links

• NCBI BLAST pagehttp://www.ncbi.nlm.nih.gov/BLAST/

• The NCBI Query Tutorialhttp://www.ncbi.nlm.nih.gov/Education/BLASTinfo/

query_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

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