LOBSA

LOCAL BLAST SEARCH ACCELERATOR

LOCAL BLAST SEARCH:

Test Data: Sequences.zip (To be unzipped in the Blast Folder)

Sample Output: Result (right click and select "save target as")

Other programs from NCBI used in this applications are:

1)  blastall.exe (1.65 MB)

2) formatdb.exe (1.37 MB)

Instructions:

To get started you need the blastall.exe and formatdb.exe (From NCBI).

For the programs to work without modifying the paths, the whole folder “Blast.zip” should be unzipped to a folder "Blast" moved under the “C:” directory.

For questions or comments please contact: Imed Ben Chouikha  bchouikh@gmu.edu

I. Step one:  Blasting

1) Download the database that you want to blast against, for example the NT database from NCBI. If you want to use a local database, store all the sequences in a text file.

The file provided by NCBI is a zipped (nt.gz) file so you have to unzip it.

2) At the DOS prompt (which you can get to from windows by choosing: Start, Run, then typing: command), run formatdb.exe to create a local database from that text file or the downloaded database. 

Usage:

            formatdb –t databasename –i inputfile –p F

databasename is the name you want to give to your database

inputfile is the name of the text file that contains your sequences or the name of the database that you downloaded from GenBank (technically also a text file of sequences).

Examples:

 1)            formatdb –t nt –i nt –p F

2)                formatdb –t snc –i inputfile –p F

More about formatdb.exe information and command options can be found here:

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/formatdb.txt

3) Open the file BlastList.pl (using Notepad or your favorite text editor)

Make the small changes as instructed in the file then save it.

These are the only two changes you might need to do.

4) Run BlastList.pl as follows:

            c:> cd Blast

            c:\>Blast\perl BlastList.pl

The file BlastList.pl automatically creates a batch file “DosBlast.bat” depending on the list of the sequence to be blasted.

5) Run DosBlast.bat

            c:\>Blast\ DosBlast.bat

DosBlast.bat is the actual file that does the blast search.

II. Step two: Extracting data from blast results

6) Move all the resulting ".txt" files to BlastOut

7) Go to the directory BlastOut

            c:\>Blast\  cd  BlastOut

8) Run Hits.pl      

             c:\>Blast\BlastOut\perl  Hits.pl

That will move the files that returned no hits to a different directory

9) Run DataExt.pl

            c:\>Blast\BlastOut\perl  DataExt.pl

The output will be written to the file Blasted.txt.

With Excel open (using tab delimited) the file Blasted.txt. 

It contains a summary of the blast results that you can save, edit, etc.

Direct questions to: bchouikh@gmu.edu