Download UNIREF database BLAST T COFFEE

Question

[charlotte.crauwels]

Hi all,

I'm trying to run T COFFEE with the mode -psicoffee and taking into account the transmembrane parameters. Therefore I need BLAST and a Uniref database. I'm struggling with the installation of the databse.

• I have installed T COFFEE and BLAST. Both seem installed correctly as I get: -when I run 't-coffee': "####### Compiling the list of available methods ... (will take a few seconds)

<h6># Methods For which an Interface is available in T-Coffee</h6>

You must install the packages yourself when required (use the provided address) Contact us if you need an extra method to be added [[e-mail]]

** Pairwise Sequence Alignment Methods:"

-when I run 'blastn': "BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified Please refer to the BLAST+ user manual."

• I have downloaded Uniref50.fasta.gz and gunzip it in a directory '/mnt/c/Users/charl/Desktop/T_COFFEE/'.

• I have done "export BLASTDB='/mnt/c/Users/charl/Desktop/T_COFFEE/' "

• When I run "blastdbcmd -db UNIREF50 -info" I get the following: Database: UNIREF50 51,333,317 sequences; 14,570,049,110 total residues

Date: Apr 11, 2022 5:34 PM Longest sequence: 45,354 residues

BLASTDB Version: 4

Volumes: /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.00 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.01 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.02 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.03 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.04 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.05 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.06 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.07 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.08 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.09 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.10 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.11 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.12 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.13 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.14 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.15 /mnt/c/Users/charl/Desktop/T_COFFEE/UNIREF50.16

• HOWEVER when I run "t_coffee GPCR_A_db.fasta -mode psicoffee -template_file PSITM -blast_server LOCAL -protein_db UNIREF50" I keep getting the same error: ERROR: Database UNIREF50 not available

Could you please help me sort this out?

Thank you, Charlotte

[charlotte.crauwels]

I just ran blastp using the installed database and using 1 sequence as query and it worked. Therefore, the database seems correctly installed... It seems like the problem is with t_coffee not finding the database...