What is Blast

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What is Blast
What/Why Standalone Blast
Locating/Downloading Blast
Using Blast
You need Your sequence to Blast and the
database to search against
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(No Transcript)
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The BLAST Family
Similarity search programs
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• Why Standalone Blast

The main advantage of Standalone Blast is to be
able to create and Blast your own databases

• Create a folder called Blast on your C/ drive to
  store the downloaded file

• Get Blast Here ?

http//www.ncbi.nlm.nih.gov/

• Scroll Down To Here ?

• Click FTP site

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• Click Here ?

Both Mac Win

• Click Executables

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• Click Latest ?

Both
MAC

• Choose32-win32..?
• Or Mac userschoose
• 32-linux.tar

Win
Click Save, then save the file in the Blast
folder you created earlier
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• Go to the Blast directory cd c/ then cd
  /Blast Windows Install ./blast-2.2.20-ia32.win
  32.exe
• MAC Install tar zxf blast-2.2.20-ia32-linux.t
  ar.gz(MAC you may find that an additional
  folder was created blast-2.2.20. In there you
  will find the folders below)

• In the Blast directory there will now be 3 new
  folders

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
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• Create the configuration files

We may skip this slide
In some instances, it may be necessary to restart
your computer
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• NOW YOUR BLAST PROGRAM HAS BEEN INSTALLED

Test Blast using the single sequence and database
provided Change to the BioDownload directory
where your database and query sequence is stored.

• Formatdb

Prepare the database before Blasting
Dont Type formatdb -i myDbase -p F
/cycgdrive/c/Blast/bin/formatdb -p blastn d
./TA496Seq1.txt -i ./TomatoSequence.seq o
out_tomato_blast
-i the file to create into a searchable
database -p T protein database and F
nucelotide database
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• Formatdb creates index files

.nhr .nin .nsq
Output Files with these extensions

• Blast

blastall -p blastn -d myDbase -i test.seq -o
test.out
/cycgdrive/c/Blast/bin/blastall -p blastn -d
./TA496Seq1.txt -i ./TomatoSequence.seq o
out_tomato_blast
blastall access all blast programs blastn
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
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• Additional Blast Parameters

e-value e

• Output of Blast Files Parsing

• Additional Blast Documentation