I have a local copy of the NR protein database to run blastp. I'm interested in analyzing a specific subset of prokaryotic genes. I've already extracted prokaryotic proteins from the NR database using the following steps:
1. Extracting proteins from bacteria and archaea taxids:
blastdbcmd -db nr -taxids 2,2157 -dbtype prot -out prokaryote_sequences.fasta
2. Creating a BLAST database from the extracted sequences:
makeblastdb -in prokaryote_sequences.fasta -dbtype prot -out nr_prok
Now, I need to further subset this database to include only specific genes of interest, such as rpoB. However, I suspect that a simple grep on the FASTA headers won't be sufficient because not all rpoB sequences might have "rpoB" in their headers.
My Question:
What is the best way to filter my custom BLAST database to include only the proteins of specific genes like rpoB?
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You could
blastwith the gene of interest against this custom DB and then extract the ID's you need as fasta to create another subset database.