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TransDecoder is a commonly used program for extracting likely coding regions from transcriptome assemblies, which does the following to make a call: TransDecoder identifies likely coding sequences based on the following criteria: a minimum length open reading frame (ORF) is found in a transcript sequence a log-likelihood score similar to ...


Yes, there are: this is a feature of bacterial intrinsic termination. The mechanism of pausing is not as you describe, though. In bacterial transcription, two forms of termination are recognised (to my knowledge): Intrinsic termination, consisting of a hairpin and a stretch of Uridines. Rho-dependent termination, consisting of a 'loading' site for ...

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