Use BLAST Command Line Applications to run a folder of many sequences against a database
I am quite new to using the BLAST Command Line Applications and would love any and all help. I am trying to use the application to run many sequences stored in a folder against a database I have created but am not sure exactly how to do this or if I am on the right track.
I downloaded and set up BLAST from NCBI using the Standalone set up for windows instructions online. From these instructions I have created a database that I want to Blast multiple sequences against using the code “makeblastdb -in dbelasmo_full.fa -parse_seqids -blastdb_version 5 -title “Elasmobranchii genomes full” -dbtype nucl”. The data was from complete genomes I downloaded from NCBI. I have been able to run single sequences against this database using “blastn –db elasmo_full.fa –query zAsic4.2_4.fa -perc_identity 50 -outfmt 7 -max_target_seqs 5” (I set the perc_identity low as a start point to find anything even remotely similar and will increase it in subsequent searches).
I am wondering if there is a code to blast a folder of .fa files, as opposed to individual files, against this database I created? I was hoping to save all the small sequences in one folder to save time rather than running them one by one.
Thanks in advance for any help or advice.
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