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:– infer functional and evolutionary relationships
between sequences– Identify members of gene families
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
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)
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)
Using BLAST – Choosing the BLAST Program
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
Using BLAST – Choosing the Database to Search
Using BLAST – Choosing the Search Parameters
BLAST Output – The Report Header
BLAST Output – Graphical Overview
BLAST Output – Another Example of the Graphical Overview
BLAST Output – Report Descriptions
BLAST Output – Pairwise Sequence Alignment(s)
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/
Other Helpful Links
● BLASThttp://blast.ncbi.nlm.nih.gov/Blast.cgi
● NCBIhttp://www.ncbi.nlm.nih.gov/
● VMD Tutorialhttp://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/vmd-tutorial-2009.html
● VMD User's Guidehttp://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html
● MEGAhttp://www.megasoftware.net/
● CLUSTALhttp://www.genome.jp/tools/clustalw/