Trinity Assembly, Isoforms vs. Paralogs?

BGould · 03-18-2012, 07:49 AM

Hello Everyone,
I am in the midst of going through a denovo non-model plant transcriptome assembly using Trintiy. I have so far been unable to find references on strategies for differentiating between very similar parologus genes and isoforms (alternative splice forms) of the same gene in the output from the assembly. The assembly is from a heterozygote, so there is also the possibility of different alleles of the same gene. Does anyone know of any references or strategies (or maybe other Threads here that I missed) for picking apart the various layers of similarity in denovo assemblies?

Any advice would be much appreciated!

Billie

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03-18-2012, 07:49 AM	#1
BGould Junior Member Location: New York Join Date: May 2010 Posts: 9	Trinity Assembly, Isoforms vs. Paralogs? Hello Everyone, I am in the midst of going through a denovo non-model plant transcriptome assembly using Trintiy. I have so far been unable to find references on strategies for differentiating between very similar parologus genes and isoforms (alternative splice forms) of the same gene in the output from the assembly. The assembly is from a heterozygote, so there is also the possibility of different alleles of the same gene. Does anyone know of any references or strategies (or maybe other Threads here that I missed) for picking apart the various layers of similarity in denovo assemblies? Any advice would be much appreciated! Billie