Blast Against Pdb Standalone Version

Question

[Reyhaneh]

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.

Answer 1

[Reyhaneh]

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.

Answer 2

[Chris]

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.

[Rm]

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

[Michael Schubert]

or: makeblastdb for database creation with NCBI BLAST+

[Reyhaneh]

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;

[Reyhaneh]

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.