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  • Extration -option for blastdbcmd command

    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.


  • #2
    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..
    Last edited by rhinoceros; 08-12-2013, 10:32 PM.
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