Question: Blast Against Pdb Standalone Version
0
gravatar for Reyhaneh
7.3 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

Hi

I have always used the online service of pBlast and now I am a bit confused since I want to use its standalone version. My aim is to blast a protein fasta sequence against PDB and save all the pdb codes of the resulted proteins. I am confused which files I do require from (ftp://ftp.ncbi.nih.gov/blast/) and what commands I need to use(My platform is Windows). I would be thankful if you can guide me on this.

I have read the available documents but wasn't able to get what I want.

Thanks for you help in advance.

blast • 4.4k views
ADD COMMENTlink written 7.3 years ago by Reyhaneh480
1
gravatar for Chris
7.3 years ago by
Chris1.6k
Munich
Chris1.6k wrote:

You need the fasta file that contains all pdb sequences, it's called pdb_seqres.txt and could be found somewhere at their ftp server. Using that, you create a blast database with 'formatdb' (in the blast package). After that, you can run your blast searches against that db. Take a look at the man page of e.g. 'blastpgp' when you want to conduct a PSI-Blast run.

ADD COMMENTlink written 7.3 years ago by Chris1.6k

ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

ADD REPLYlink written 7.3 years ago by Rm7.8k

or: makeblastdb for database creation with NCBI BLAST+

ADD REPLYlink written 7.3 years ago by Michael Schubert6.9k

Thanks for you help. I am using Blast+ version blast-2.2.25+ and the new package has makeblastdb instead of formatdb. when I run the command:

makeblastdb -in pdb_seqres.txt -out testdb -dbtype prot

I get the Error: Unable to open input pdb_seqres.txt as either FASTA file or BLAST db

Do you have any idea how I can solve it?

Cheers;

ADD REPLYlink written 7.3 years ago by Reyhaneh480

I have made it work the problem is that I have to take pdb_seqres.txt under the blast-2.2.25+ directory in order for it to work. makeblastdb -in pdb_seqres.txt I only used this command to get the new database.

ADD REPLYlink written 7.3 years ago by Reyhaneh480
1
gravatar for Reyhaneh
7.3 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

I have solved the problem. I had installed Blast.2.2.5+ from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ and then I downloaded "pdbaa" database from (ftp://ftp.ncbi.nih.gov/blast/db/). you also need to extracted all "nr.##.tar.gz" files and place them in the Blast.2.2.5+ folder. Now you can generate the output using the following command:

blastp –query inFile.txt –db pdbaa –out output.txt

where the inFile.txt is a protein in FASTA format. the result will be in output.txt.

ADD COMMENTlink written 7.3 years ago by Reyhaneh480
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