I am building a custome databse for all viral sequnces so i could run local blast to seperate viral related contigs from host's whole genome sequnce.
makeblastdb -in /path/sequences.fasta -dbtype nucl -out /path/DATABASE_NAME -title DATABASE_NAME
I had created a set of scripts to do the exact same thing maybe they can help you :)
https://github.com/mbshah/ncim-bioinfo/blob/master/virCodes/retrieve2.pl
to retrieve the Viral information from NCBI
(It uses a few other scripts from the same folder:
https://github.com/mbshah/ncim-bioinfo/blob/master/virCodes/dbmaker.pl
https://github.com/mbshah/ncim-bioinfo/blob/master/virCodes/gb_utils_xml.pl
)
P.S. I made the scripts a few years back and requires blast+ installed, and even if it doesn't work it should give you some ideas.
I was downloading GB files instead of fasta sequences because i planned to use them for annotating the results as well.
I also try to make my oun database like Abhijeet Singh did, but why the output provides N/A column of sscinames? I tried to add taxon_map file to add taxonid info, but blast use numerology of its common database while my database is not a subset of common blast database.. What can I do?
Irfan Ahmed Manan Shah
Irina Bulusheva
https://www.ncbi.nlm.nih.gov/sites/books/NBK569841/
https://www.biostars.org/p/15602/
I saw it. Unfortunately, it only works on taxa from the blast base, not de novo seqs and names
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