[maker-devel] collecting protein sequences as evidences

[Michael Campbell]

Hi Quanwei,

(1) When I use uniprot I use SWISS-prot and not tremble.
(2) I don’t merge files together. I just pass them all to MAKER as a comma separated list.

Thanks,
Mike

> On Jan 31, 2017, at 12:36 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> I wonder what's the best way to collect protein sequences for gene annotation of a de novo genome assembly. 
> (1) My first choice is to get protein sequences of human and mouse from UniProt. At this step, I am not clear whether I should download the reviewed ones (i.e., SWISS-prot) or automatically annotated ones (i.e., TrEMBL). 
> (2) On ther other hand, I also get protein sequences from NCBI, should I just simply merge those fasta files. Does it matter if there are redundancies? And also, if I get protein sequences from different sources, they may not have the same quality. Do I need to do something before I integrate protein sequences from different sources? 
> 
> Many thanks
> 
> Best
> Quanwei
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