Question: Creating blast database blast+
0
gravatar for jeevansai502
3.1 years ago by
jeevansai5020 wrote:

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 • 1.7k views
ADD COMMENTlink modified 3.1 years ago by Buffo1.8k • written 3.1 years ago by jeevansai5020
0
gravatar for Buffo
3.1 years ago by
Buffo1.8k
Buffo1.8k wrote:

You may try using concatenate "cat":

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

Then you can make your complete DB.

ADD COMMENTlink written 3.1 years ago by Buffo1.8k

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by st.ph.n2.5k

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

ADD REPLYlink written 3.1 years ago by jeevansai5020

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax90k

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.

ADD REPLYlink written 3.1 years ago by jeevansai5020

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.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax90k
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