This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Creating blast database blast+

I want to create a database consisting of all many nucleotide sequence fasta files in blast+ linux tool ,but the tool only allows me to create database for every fasta file,so i will get multiple databases but not a single one,Is there any way i can achieve task.

blast+ blastdb
• 3,299 views • link
updated by Buffo Buffo • written by jeevansai502 • jeevansai502

1 answer

You may try using concatenate "cat":

cat file1.fasta file2.fasta file3.fasta > my_all_files.fasta

Then you can make your complete DB.

• 0 views • link
written by Buffo Buffo

Make sure each fasta file has unique headers, that there are no duplicates across each file.

• 0 views • link
written by st.ph.n st.ph.n

Now if i want to add a new file to the database,i won't be able to do so

• 0 views • link
written by jeevansai502 • jeevansai502

You can create a new source file and then create a new database from that.

• 0 views • link
written by GenoMax GenoMax

so you are saying that i have to concatenate all files with new one and then make database again,but this method is untidy.I want to create a single database which will allow me to add new files or sequences easily to it .The number of files or sequences is huge.

• 0 views • link
written by jeevansai502 • jeevansai502

In that case you could use blastdb_aliastool utility to aggregate individual databases.

 3) Alias file creation (aggregating BLAST databases):
      Creates an alias for multiple BLAST databases. All databases must be of
      the same molecule type (no validation is done). The relevant options are
      -dblist and -num_volumes.

It may still become unwieldy if you intend to do this multiple times. Check blastdb_aliastool -help for more info.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this