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Local Blast Database

I need to blast one protein query file against 150 nucleotide files. at first I tried Blast but it says there is not database, I created a database with one of the 150 files and blasted against it, it worked!

So How do I loop through the 150 files and create a database of each of them so that the query file can blast against them one after another?

makeblastdb -in 1st_file.fasta -dbtype nucl -out 1st_file_BlastDB -parse_seqids

blast sequence alignment
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written by Nano • Nano

3 answers

You should make one database of all 150 by first concatenating the fasta files into one long one.

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updated by Ram Ram • written by karl.stamm karl.stamm

You could possibly use Bioedit. Put all files in a single one and select the "Create local protein/nucleotide database".

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written by gbdias gbdias

The problem with concatenation is that it will produce a single file, I am required to find the expression level of each query sequence from each of file among the 150 files. if i concatenate them, the result wont specify the expression on each file, so i need to create a database for every file and blast against them. Later i will need to see which query sequence is expressed in at least 90% of the files. I hope this is clear

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written by Nano • Nano
You haven't answered the question, this is not a forum. Biosters is q&a. You mean to comment on the answers directly. As I am commenting on yours. It's wrong. With one database of many sequences, the query provides a number of hits to each site. Just ask blast to return the target of a hit in a table. Not sure what that has to do with expression, you may be entirely on the wrong track. There are easier ways to find common expression.
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written by karl.stamm karl.stamm

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