setting databases or resetting databases

sequenceserver
#1

machine:~> sequenceserver -l
nucleotide: /mcdb/mondex_blast_data_extraction/extracted_files/mondex.nt /mcdb/mondex_blast_data_extraction/extracted_files/mondex.nt
protein: /mcdb/mondex_blast_data_extraction/extracted_files/mondex.aa /mcdb/mondex_blast_data_extraction/extracted_files/mondex.aa

as you can see it’s listing the same databases twice
how do i reset sequenceserver so that it only lists one?

#2

I believe the first path you see is actually the title of the database and the second path you see is the path to the database. e.g. I see the following (bold are my DB titles)

protein: RGAPv7 all pep /mnt/blast_dbs/new/RGAPv7_all_pep
nucleotide: RGAPv7 all seq /mnt/blast_dbs/new/RGAPv7_all_seq

#3

Nathan is right - in your case database title is the same as path.

To reformat your sequences for BLAST, go to your database directory and delete nih, nin, pih, pin etc. files. You can use the command below to do so if you use zsh:

rm **/*.{nhd,nhi,nhr,nin,nog,nsd,nsi,nsq,phd,phi,phr,pin,pog,psd,psi,psq}

Then run,

sequenceserver -m -d /my/database-dir

Override the suggested title when it prompts you. Run “sequenceserver -l” afterwards and the listing should look as expected.

Priyam

#4

Thank you for the information.
It looks correct now.