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:– 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/