What are the techniques to determine transcription binding sites (transcription start sites) in the genome of a non-model organism?

Jose Maria Aguilar-Camacho @Jose-Aguilar-Camacho

01 January 1970 1 10K Report

I am working with a non-model organism and we generated a complete genome that is annotated. How can you determine the transcriptions start sites in this genome? Is there any bioinformatic way to do it (software)? or Do I need to do an experiment to identify these sites in the genome? I know that CAGE seq and CHIP-seq are good techniques to do that. But I am not sure if there is a computational tool to identify these sites.

Gregory Dressler

If you have the genome sequence then I would do an RNA-Seq from your organism, trying to get as representative and as much RNA as possible. Map all the reads to your genome and the start sites should become clear as the most 5' end of a transcript.

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