Extration -option for blastdbcmd command

[laboder]

Hi,

I am interested in getting associated with the resistance of cadmium from the sequences of contigs noted on MG_RAST and recognized for this function genes. the sequence contigs are derived from the de novo assembly of metagenome data contaminated with heavy metals lakes.

I did a BLASTN, using the command: blastn-query with the optional 6-outfmt blasn.out-out, to finally have the array that contains the NCBI id of hits related to the resistence of cadmium.

When I would have the fasta file id NCBI genome sequences, using the blastdbcmd order, I get all the complete genome of organisms that have the genes of interest, but I want to know if there is an option in blastdbcmd command used to extract just the genes involved in CDs or resistence cadmium: CzcA CzcB, Czcc, CzcD.

Thanks,
LaboDer.

[rhinoceros]

You could probably extract your stuff straight from MG-RAST. As to your question, with blastdmcmd you simply provide a list of IDs. It's up to you to produce that list. If 'CzcA CzcB, Czcc, CzcD' appear in sequence titles, you could probably awk your way.. see the blast manual..