How to identify secondary metabolite biosynthetic genes from set of contigs?
I had get a set of contigs assembled by using trinity and I'm ask to identify genes that responsible for producing secondary metabolite, so how to identify it from set of contigs? Which annotation tools can help to do this? My sample is from type of fungal... Thanks~
1 answer
Several (most?) secondary metabolites are produced by clusters of genes, so you won be able to predict individual metabolites from transcriptome alone. But you could download the gene cluster from antiSMASH, set up a local blast database and blast your transcriptome against it.
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