I am interested in determining the functonal diversity of PAH-dioxygenase gene across environmental gradients. i have the metagenomic sequences of my sample from Illumina Miseq platform. i don't understand how i can use primers to search through the sequence data. i will appreciate any help. Thanks for your anticipated help
One option is to analyse if using dedicated databases you have matching similar sequences related with the genes involved in catabolism. We published some options and datasets recently. http://www.ncbi.nlm.nih.gov/pubmed/25468931 and the concept is coming from http://www.ncbi.nlm.nih.gov/pubmed/22515215
I agree with Suma, once you have the sequence, QC them, then define your best database to use as reference. Then, there are pipelines to quantify taxonomy abundances in your dataset (we use Qiime but Mothur work as well). Those work if your sequences are from amplicons. Or you can use MEGAN if your data are from genomic sequences.
thanks alot, it's a metagenomic data. am interested in determining pah~dioxygenase distribution. I found out i u could use fraggenescan. any idea how to go about if it?
Sorry, never used it.
In your case, I would look at MEGAN5 or to assembly the sequences using Mega-Hit or metagenomic SPAdes, than annotate the contigs with Prokka and analyse the distribution of your gene.
Regards
- Badges
- Science method