What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your...

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What is Blast What is Blast What/Why Standalone What/Why Standalone Blast Blast Locating/Downloading Locating/Downloading Blast Blast Using Blast Using Blast You need: Your You need: Your sequence to Blast and sequence to Blast and the database to search the database to search against against

Transcript of What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your...

Page 1: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 2: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to 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

Page 3: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

Similarity search programsSimilarity search programs

The BLAST FamilyThe BLAST Family

blastpprotein/protein

blastnnucleotide/nucleotide

blastxnucleotide/protein

tblastnprotein/nucleotide

tblastxnucleotide/ nucleotide

Page 4: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 5: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

Click Here Click Here

Click ExecutablesClick Executables

Both Mac & Win

Page 6: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 7: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 8: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 9: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 10: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

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

Page 11: What is Blast What/Why Standalone Blast Locating/Downloading Blast Using Blast You need: Your sequence to Blast and the database to search against.

Additional Blast ParametersAdditional Blast Parameters

e-valuee-value ee

Additional Blast DocumentationAdditional Blast Documentation

Output of Blast Files & ParsingOutput of Blast Files & Parsing