What is BlastWhat is Blast
What/Why Standalone BlastWhat/Why Standalone Blast
Locating/Downloading BlastLocating/Downloading Blast
Using BlastUsing Blast
You need: Your sequence You need: Your sequence to Blast and the database to Blast and the database to search againstto search against
National Center for BiotechnologyInformation (NCBI) – 1988 BLAST – Basic Local Alignment Search Tool
Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases
NCBI maintains several large annotated databases that are freely available to the public for download.YOU MAY WANT TO USE YOUR OWN DATABASE
Similarity search programsSimilarity search programs
The BLAST FamilyThe BLAST Family
blastpprotein/protein
blastnnucleotide/nucleotide
blastxnucleotide/protein
tblastnprotein/nucleotide
tblastxnucleotide/ nucleotide
http://www.ncbi.nlm.nih.gov/
Why Standalone BlastWhy Standalone Blast
Get Blast Here Get Blast Here Scroll Down To Here Scroll Down To Here Click Click FTP siteFTP site
Create a folder called Blast on your C:/ Create a folder called Blast on your C:/ drive to store the downloaded filedrive to store the downloaded file
The main advantage of Standalone Blast is to be able The main advantage of Standalone Blast is to be able to create and Blast your own databasesto create and Blast your own databases
Click Here Click Here
Click ExecutablesClick Executables
Both Mac & Win
Click Latest Click Latest
ChooseChoose32-win32..32-win32..
Or Mac usersOr Mac userschoosechoose
32-linux.tar…32-linux.tar…
Click Save, then save the file in the Click Save, then save the file in the Blast folder you created earlierBlast folder you created earlier
MAC
Win
Both
Go to the Blast directory: Go to the Blast directory: cd c:/ cd c:/ then then cd /Blastcd /Blast Windows Install: Windows Install: ./blast-2.2.20-./blast-2.2.20-ia32.win32.exeia32.win32.exe
MAC Install: MAC Install: tar zxf blast-2.2.20-ia32-linux.tar.gztar zxf blast-2.2.20-ia32-linux.tar.gz(MAC: you may find that an additional folder was (MAC: you may find that an additional folder was created “blast-2.2.20”. In there you will find the created “blast-2.2.20”. In there you will find the folders below)folders below)
In the Blast directory there will now be 3 new In the Blast directory there will now be 3 new foldersfolders
All Blast files are located here
Blast documentation in html format. Best viewed in a web browser
Algorithms for statistical analysis and sample search databases
Create the configuration filesCreate the configuration files
In some instances, it may be necessary to restart your In some instances, it may be necessary to restart your computercomputer
Go to your Windows directory (Win)Go to your Windows directory (Win)
cat > ncbi.inicat > ncbi.ini
[NCBI] [NCBI]
Data="C:\Blast\data\“Data="C:\Blast\data\“
TO SAVE & QUIT PRESS CTRL D
Go to your root directory (Mac)Go to your root directory (Mac)
cat > .ncbirccat > .ncbirc
[NCBI] [NCBI]
Data=/Blast/dataData=/Blast/data
SAVE & QUIT PRESS CTRL Z
NOTE: This step appears to be unnecessary, and even NOTE: This step appears to be unnecessary, and even problematic for newer versions of Windows and MAC OS problematic for newer versions of Windows and MAC OS
XX
In some instances, it may be necessary to restart your computerIn some instances, it may be necessary to restart your computer
NOW YOUR BLAST PROGRAM HAS BEEN INSTALLEDNOW YOUR BLAST PROGRAM HAS BEEN INSTALLED
Test Blast using the single sequence and database Test Blast using the single sequence and database providedprovided**** Change to the BioDownload directory where your Change to the BioDownload directory where your database and query sequence is stored.database and query sequence is stored. FormatdbFormatdb Prepare the database before BlastingPrepare the database before Blasting
To executeTo execute formatdb -i myDbase -p F you formatdb -i myDbase -p F you need the correct pathneed the correct path
-i the file to create into a searchable database
-p T = protein database and F = nucleotide database
/cygdrive/c/Blast/bin/formatdb -i ./TA496Seq1.txt –p F
Formatdb creates index filesFormatdb creates index files
.nhr.nhr
.nin.nin
.nsq.nsq
Output Output Files with Files with these these extensionsextensions
BlastBlastblastall -p blastn -d myDbase -i test.seq -o
test.out
blastall: access all blast programsblastn: select the blastn program since query and database are nucleotide-d: the database to blast-i: the query sequence(s) to blast-o: the name of the file to store your blast results
/cygdrive/c/Blast/bin/blastall -p blastn -d ./TA496Seq1.txt -i ./TomatoSequence.seq –o out_tomato_blast
Additional Blast ParametersAdditional Blast Parameters
e-valuee-value ee
Additional Blast DocumentationAdditional Blast Documentation
Output of Blast Files & ParsingOutput of Blast Files & Parsing