Manual for using the stand-alone Blast Search on the server of Lab Hochholdinger:


1.Creating your own database for blast:

Run the SA-Blast.lnk in this folder (X:\Lab_Hochholdinger\SA-Blast)

A window running cmd.exe will open. The bottom line of that windows should look like
"X:\Lab_Hochholdinger\SA_Blast>"

In cmd.exe type: cd databases [enter]

- 	Create a fasta-file containing all your accessions and sequence data. A nice example for such a
	fasta-file is the example.txt. These files can be set up using the windows editor or by using the perl
	script.
-	Give that fasta-file a name that doesnt exist so far (e.g. xy.txt) and save it in
	"X:\Lab_Hochholdinger\SA_Blast\databases". xy should be the name of the final database.
-	In the cmd-window type (or copy): "formatdb -i xy.txt -p F -o T -n xy" [enter]
	This will create up to seven database-files named "xy.*". The name of your database will be "xy".
-	Create a new subfolder named "xy" and move all of your database files in there.
-	You are done creating yout database. Please enter the name and description of your database in database.xls
	located in "X:\Lab_Hochholdinger\SA_Blast\databases"


2. Running a local blast search against your database of interest:
a. Preparing your query-file

Run the SA-Blast.lnk in this folder (X:\Lab_Hochholdinger\SA-Blast)

A window running cmd.exe will open. The bottom line of that windows should look like
"X:\Lab_Hochholdinger\SA_Blast>"

In cmd.exe type: cd bin [enter]

-	In Windows copy all your database-files into "X:\Lab_Hochholdinger\SA_Blast\bin"
-	Create a file containing one or more "querys" (sequences you want to blast against your database)
	This file should be in fasta-format starting with an ">" and the name or accession of your sequence.
	The second line should contain the sequence for that name/accession. You can run single or multiple
	blast-searches at once by entering these sequences into your fasta-file. Multiple sequences should
	be seperated by blank lines. Have a look in ex1in.txt for single sequences or ex2in.txt for multiple
	sequences. Ex1out.txt and Ex2out.txt will give you an example for the output of your search.
-	Save your query-file (e.g. "abc_in.txt") and copy it to "X:\Lab_Hochholdinger\SA_Blast\bin".

b. Running the blast search
-	Go back to cmd.exe. The bottom line should look like "X:\Lab_Hochholdinger\SA_Blast\bin>"
-	Type:

	blastall -p blastn -d xy -i abc_in.txt -o abc_out.txt [enter]

	IMPORTANT: Replace xy by the name of your database! abc_in.txt is your query-file! abc_out.txt will
	be the Blast-Output-file created by the search!

-	If you get too many hits with low e-values, try the following command-line:

	blastall -p blastn -e 0.0000000001 -d xy -i abc_in.txt -o abc_out.txt [enter]

	This will exclude all hits with an e-value higher than e-10!

	To understand the difference between these two commands, have a look in ex1out.txt and ex2out.txt.
	ex2out.txt has been created using the standard e-cut-off, ex1out.txt with -e 0.0000000001.
-	Whatever command line you have chosen, an output-file (e.g. abc_out.txt) has been created containing
	the results of your search. Copy it it to some other folder. Congratulations, you are almost done!
-	IMPORTANT: Please delete ALL your database- query- and result-files in
	"X:\Lab_Hochholdinger\SA_Blast\bin>"! Otherwise the bin-folder will get messed up soon! Be sure that
	you saved your database in the databases-folder previously.

Have fun using the blast tool.
Nils

P.S.: If you find any type errors or mistakes: Feel free to keep them, theyre yours! :-)