Generaing seq.dat and seq.txt files with REMO

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user366312
Posts: 2
Joined: Sat Oct 29, 2022 2:35 pm

Generaing seq.dat and seq.txt files with REMO

Post by user366312 »

I am trying to generate seq.dat and seq.txt files myself, so I can use them with REMO.
I am using mkseq.pl script.

The following was my command:

Code: Select all

user_name@server_name:~/spatial/reconstruction_tools/remo_v2$ perl mkseq.pl /home/spatial/input_pdb/pdb1a6j.pdb 1
PSIPRED finished
user_name@server_name:~/spatial/reconstruction_tools/remo_v2$
This command generated four files:
  • seq.dat
  • protein.fasta
  • psitmp27331007f0101.blast
  • psitmp27331007f0101.fasta
seq.dat is totally empty (therefore, Gmail didn't allow me to attach that to this email).
psitmp27331007f0101.blast is also practically empty.

I have a few questions in this regard:
  • Is it normal for the psitmp27331007f0101.blast to be empty in this case?
  • What do you think I should change to successfully generate seq.dat file?
  • Do I need to generate one seq.dat file for each PDB file to be used with ./REMO.pl command? If so, how can I do that, as all seq.dat files are saved with the same name in the same directory?
jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: Generaing seq.dat and seq.txt files with REMO

Post by jlspzw »

Dear user,

In mkseq.pl you need change the first serval lines

$libdir ="$path"; #####Chainge to specify path
$dbname ="$libdir/nr/nr.filter"; # The name of the BLAST data bank
$ncbidir="$libdir/blast/bin"; # Where the NCBI legacy blast programs have been installed
$execdir="$libdir/psipred24/bin"; # Where the PSIPRED programs have been installed
$datadir="$libdir/psipred24/data"; # Where the PSIPRED data files have been installed

first, you need to download the nr database that can be used by psiblast and psipred,

we recommend you download this one http://zhanglab.ccmb.med.umich.edu/library/nr.tar.gz

then download the program of blast (blast-2.2.26 is recommaded) and psipred package.

Then put blast, psipred, nr database to a same folder, then change those lines correspondingly.

Best
IT Team
user366312
Posts: 2
Joined: Sat Oct 29, 2022 2:35 pm

Re: Generaing seq.dat and seq.txt files with REMO

Post by user366312 »

There is no file named [nr.filter] inside [nr.tar.gz].

I have the following files inside [nr.tar.gz] ---

Code: Select all

user_name@server_name:~/spatial/reconstruction_tools/nr$ ls
nr         nr.00.pnd  nr.00.psq  nr.01.pnd  nr.01.psi  nr.02.pin  nr.02.psd  nr.03.phr  nr.03.pni  nr.03.psq
nr.00.phr  nr.00.pni  nr.01.phr  nr.01.pni  nr.01.psq  nr.02.pnd  nr.02.psi  nr.03.pin  nr.03.psd  nr.pal
nr.00.pin  nr.00.psi  nr.01.pin  nr.01.psd  nr.02.phr  nr.02.pni  nr.02.psq  nr.03.pnd  nr.03.psi  nr.psd
user_name@server_name:~/spatial/reconstruction_tools/nr$
And, after appropriately modifying the [myseq.pl] file, I am getting the same result as before.

Keeping the above files in [nr/nr.filter/*.*] makes no difference.

Am I doing anything wrong with the directory structure of [remo_v2]?

Code: Select all

/home/user_name/spatial/reconstruction_tools/
.
└── blast
│   └── bin
│   └── data
│   └── doc
└── nr
│   └── nr.filter
└── psipred
│   └── bin
│   └── BLAST+
│   └── data
│   └── example
│   └── src
└── remo_v2
│   └── SRC
│   │   └── example

jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: Generaing seq.dat and seq.txt files with REMO

Post by jlspzw »

Dear user,

you can change $dbname ="$libdir/nr/nr.filter"; to $dbname ="$libdir/nr/nr";


Best
IT team
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