getting information from NCBI genebank files

Question

[saadleeshehreen]

Hi, I am interested to know about the presence of a specific protein called "anti restriction" in a list of ~600 genomes of different species of bacteria. It can be find from the NCBI genebank files. Manually checking those 600 genomes is time-consuming. Any suggestions on how can I know which of these genomes contain this specific protein? Thanks in advance

[GenoMax]

Two possible options:

1. NCBI allows you to restrict online web blast searches against certain organisms. It may not be possible to put in 600 at a time though.
2. Download the 600 genomes locally and do blast against that set. More work but feasible. You can use the method in this answer to get the genomes: A: How to download COMPLETE bacterial genomes from NCBI based on list of names?

[Fatima]

Do you already have the protein sequences?

[saadleeshehreen]

It could be any protein associated with anti-restriction. I am looking for a correlation between 'protein A' with anti-restriction proteins. I have already got 600 genomes having protein A. Now, trying to look at which of these genomes have anti-restriction proteins.

[Fatima]

I'm not sure if my suggestion is the best approach and I'm not even sure if it's feasible, but here you go:

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Archaea_Bacteria/
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Archaea_Bacteria/All_Archaea_Bacteria.gene_info.gz
cat All_Archaea_Bacteria.gene_info | grep -i -E "anti-restriction|anti restriction" > anti-restriction-list.txt
ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
gunzip nr.gz 
Then search for proteins in anti-restriction-list.txt  and find their protein sequences 
and then blast against those 600 genomes (e.g concatenate them, use makeblastdb, options _num_alignments 1 and -evalue 1e-300 in tblastn might help)