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BLAST: Basic Local Alignment Search Tool

BLAST: Basic Local Alignment Search Tool. BLAST. Finds regions of local similarity between sequences Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of the matches Can be used to:

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BLAST: Basic Local Alignment Search Tool

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  1. BLAST: Basic Local Alignment Search Tool

  2. BLAST • Finds regions of local similarity between sequences • Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of the matches • Can be used to: • infer functional and evolutionary relationships between sequences • Identify members of gene families

  3. BLAST • Most use BLAST by inputting a sequence as a query against a specified public sequence database • The query is sent over the internet and the search is performed on the NCBI databases and servers with the results posted back to the person's browser

  4. Standalone BLAST • Often utilized by biotech companies, genome scientists and bioinformatics personnel • to query their own local databases • to customize BLAST to their own specific needs • Comes in two forms: • Executables that can be run from the command line • Standalone WWW BLAST Server (allows users to set up their own in-house versions of the BLAST Web pages)

  5. BLAST variations • DNA query to a DNA database • Protein query to a protein database • DNA query query translated in all 6 reading frames to a protein sequence database • Other adaptations • PSI-BLAST (iterative protein sequence similarity searches using a position-specific score matrix) • RPS-BLAST (searching for protein domains in the Conserved Domains Database)

  6. Using BLAST – Choosing the BLAST Program

  7. Using BLAST – Entering the Query Sequence • After choosing the search we want to perform, we next need to enter the query sequence • Our example query protein >gi|4503323|ref|NP_000782.1| dihydrofolate reductase [Homo sapiens] MVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKG RINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIM QDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND

  8. Using BLAST – Choosing the Database to Search

  9. Using BLAST – Choosing the Search Parameters

  10. BLAST Output – The Report Header

  11. BLAST Output – Graphical Overview

  12. BLAST Output – Another Example of the Graphical Overview

  13. BLAST Output – Report Descriptions

  14. BLAST Output – Pairwise Sequence Alignment(s)

  15. Most of the information contained in this presentation can be obtained through the following links: • http://www.ncbi.nlm.nih.gov/books/NBK21097/ • http://etutorials.org/Misc/blast/Part+I+Introduction/Chapter+1.+Hello+BLAST/1.2+Using+NCBI-BLAST/

  16. Other Helpful Links • BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi • NCBI http://www.ncbi.nlm.nih.gov/ • VMD Tutorial http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/vmd-tutorial-2009.html • VMD User's Guide http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html • MEGA http://www.megasoftware.net/ • CLUSTAL http://www.genome.jp/tools/clustalw/

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