Eukaryotic Genome Annotation - Without ESTs or Transcriptomic or Proteomic Data
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6.5 years ago
maxwhjohn1988 ▴ 130

First off, apologies if this is a duplicate - I have searched and not found anything addressing this question, but that doesn't mean this hasn't been asked elsewhere.

I have a genome assembly, and I want to annotate some contigs of interest. The species in question is not well-studied and there are no ESTs, transcriptomes or proteomes in existence as far as I know. On top of that I am completely new to annotation and don't have anyone pointing me in the right direction.

I have read Yandell and Ence's review "A beginner's guide to eukaryotic genome annotation" https://www.nature.com/articles/nrg3174 which was very helpful in outlining the options available to me. However I feel a bit swamped by the whole topic.

I have been looking about for genome annotation pipelines but have not found any which deal with annotation in the complete absence of supporting data like RNA, protein, or ESTs.

I am well-aware that attempting annotation without these supporting data is not the best idea, but I need to do it and there's no chance of getting any extra data any time soon.

I've got as far as deciding that WindowMasker is probably the tool I will use for repeat masking (although I am not 100% confident in this decision), and beyond that I am aware that I would need to do some kind of ab initio gene prediction, presumably with several different tools, and then synthesise some kind of consensus.

Does anyone have any resources, pipelines, advice, or anything else which could help me get moving on this? I'm more or less at sea here. Thanks in advance.

Annotation Gene prediction Non-model organisms • 1.8k views
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What is your species name? Did you try Augustus. It can perform ab initio predictions but it requires a species name. See the list at the end of this page You can try using the best annotated species of the phylum in which your species of interest belongs.

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Thanks for the reply, ashish. The species is an ant, and it is not in the list unfortunately (it's not a well-studied organism and only a few groups in the world work with it).

I've spent all day getting MAKER installed with all its dependencies, since I read that it can do masking and ab initio prediction. I'll have a careful think about potential sources of extrinsic evidence to throw into the mix, too.

If anyone else reading this has any ideas of helpful suggestions, I'd still love to hear them.

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