blast two fasta files against each other 07-02-2014d1042

2014-08-29

You can blast two fasta files directly against eachother with the subject command instead of using a database.  For example:
blastp -task blastp-short -subject "clustered best motifs wo HEQWI.fa" -query HEQWI.fa -out results_07-11-2014d1029.txt

database method
{
first turn one of the fasta files (most likely the larger one) into a blast database
-example
--makeblastdb -in file1.fa -dbtype prot -title protdb -out file1

Next call a blast command to search the database with a query
-blastp -task blastp-short -db file1 -query file2.fa -out results_07-02-2014d1029.txt
--find actual files here: C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-02-2014d0933\testblast

Note: performing a blast against a database only seems to work if the command line has navigated to the directory with the database
-An alternative solution is to set a windows environment variable so that blast knows where to look for the databases.
--control panel->system and security->System->Advanced system settings->Advanced tab->environment variables->new->bariable name: "BLASTDB", value: the path to wherever you want to put all of your blast databases
---see also this ncbi help webpage: http://www.ncbi.nlm.nih.gov/books/NBK52637/
}

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