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What is Blast

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 Biotechnology Information (NCBI) – 1988 BLAST – Basic Local Alignment Search Tool.

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What is Blast

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  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

  2. National Center for Biotechnology Information (NCBI) – 1988 BLAST – Basic Local Alignment Search Tool NCBI maintains several large annotated databases that are freely available to the public for download.YOU MAY WANT TO USE YOUR OWN DATABASE Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases

  3. tblastx nucleotide/ nucleotide blastp protein/protein blastn tblastn nucleotide/nucleotide protein/nucleotide blastx nucleotide/protein The BLAST Family Similarity search programs

  4. 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

  5. Click Here  Both Mac & Win • Click Executables

  6. 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

  7. Go to the Blast directory: cd c:/ then cd /Blast Windows Install: ./blast-2.2.20-ia32.win32.exe • MAC Install: tar zxf blast-2.2.20-ia32-linux.tar.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

  8. Create the configuration files NOTE: This step appears to be unnecessary, and even problematic for newer versions of Windows and MAC OS X In some instances, it may be necessary to restart your computer In some instances, it may be necessary to restart your computer

  9. 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 To execute formatdb -i myDbase -p F you need the correct path /cygdrive/c/Blast/bin/formatdb -i ./TA496Seq1.txt –p F -i the file to create into a searchable database -p T = protein database and F = nucleotide database

  10. Formatdb creates index files .nhr .nin .nsq Output Files with these extensions • Blast blastall -p blastn -d myDbase -i test.seq -o test.out /cygdrive/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

  11. Additional Blast Parameters e-value e • Output of Blast Files & Parsing • Additional Blast Documentation

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