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  • best strategy for rRNA from shotgun?

    Hi,

    I have a 454 metagenomic sample, from which I would like to extract species frequency & diversity, among other things. I am currently using MG-RAST, with GreenGenes as my SSUrRNA reference database, 96% identity cutoff, 100 bp minimum alignment length and a e-value of 10^-5. I was wondering if anyone has some experience with doing this, and whether better parameters can be used to increase sensitivity/specificity of finding SSUrRNA in such a sample?

    Thanks,

    Iddo
    Last edited by idoerg; 01-18-2011, 07:29 AM.

  • #2
    Originally posted by idoerg View Post
    Hi,

    I have a 454 metagenomic sample, from which I would like to extract species frequency & diversity, among other things. I am currently using MG-RAST, with GreenGenes as my SSUrRNA reference database, 96% identity cutoff, 100 bp minimum alignment length and a e-value of 10^-5. I was wondering if anyone has some experience with doing this, and whether better parameters can be used to increase sensitivity/specificity of finding SSUrRNA in such a sample?

    Thanks,

    Iddo
    Hello,

    i'm doing a work similar, i think... but i used 80%identity cutoff, isn't right? I think if I use 96% a lot of sequences will not appear, right? 80% its good? or some will miss too?

    Comment


    • #3
      Originally posted by Chuckytah View Post
      Hello,

      i'm doing a work similar, i think... but i used 80%identity cutoff, isn't right? I think if I use 96% a lot of sequences will not appear, right? 80% its good? or some will miss too?
      80% for SSUrRNA is not specific enough, and basically you will be grouping all bacteria together as a single OTU

      Comment


      • #4
        Originally posted by idoerg View Post
        80% for SSUrRNA is not specific enough, and basically you will be grouping all bacteria together as a single OTU

        it is not form SSurRNA it's DNA samples, from root-soil, plant. and i need to separate from plant and fungi only.

        Comment

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