Hi all,
I am using Evigene to get the transcriptomes of my non-model organisms. However, based on some of my comparisons, it seems to me Evigene tr2aacds is only takin ATG as a potential start codon.
Does anybody have more experience on this? What is the reasoning behind removing the alternative start codons (TTG, CTG)?
1 answer
The reasoning is less about rarity than about predictability. Non-AUG initiation in eukaryotes is real, but it gets discovered by ribosome profiling rather than inferred from sequence - there's no motif that tells you a particular CTG is actually used as a start. A predictor that allowed TTG/CTG would extend a large share of ORFs upstream to the first such codon, and the false positives would swamp the handful of genuine cases. So it's a precision decision rather than a claim that alternative starts don't exist.
For your own data I'd guess 5' truncation matters more than start codon choice anyway. De novo assembled transcripts frequently miss the real 5' end, so tr2aacds ends up taking the first in-frame ATG downstream of the true one. The aa headers carry a completeness flag, so it's worth counting how many of your ORFs came out partial5 before reading much into the starts.
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my first guess would be that Evigene (don't really know that) might be focused on eukaryotic species/genomes/genes and there the ATG is the predominant startcodon, the alternative starts are very very rare in eukaryotes (they tend to be more common in prokaryotes for instance)
EviGene: http://arthropods.eugenes.org/EvidentialGene/evigene/ is for "Evidence Directed Gene Construction for Eukaryotes".