[maker-devel] Protein Evidence for teleost fish

[Carson Holt]

You can use as many proteomes as you would like.  The tradeoff is that runtime increases.  95% of runtime is just evidence alignment, so twice the evidence means about twice the runtime.  Use at least 2 related proteomes, and perhaps all of UniProt/swiss-prot, which is very well curated and will contain a number of distant outgroups for genes that are conserved across species.

—Carson




> On Oct 20, 2014, at 3:39 PM, Allison Fuiten <allisonfuiten at gmail.com> wrote:
> 
> Hello,
> 
>  
> I am currently using Maker to annotate a de novo genome assembly for a teleost fish. I would like some clarification that I am using an appropriate set of protein evidence for the annotation pipeline. For mRNA/EST evidence, I am using two independent transcriptomes (assembled with Trinity) from my specific species.
> 
>  
> For the protein evidence, I am planning on using two proteomes from closely related model teleost species from the Ensembl database. From Ensembl, you can download all protein translations for a given species either resulting from known or novel gene models which are based on transcriptome & proteome data (the ‘pep.all.fa’ file) or resulting from 'ab initio' gene prediction algorithms solely based on the genomic sequence with no other experimental evidence (‘pep.abinitio.fa’ file). I’m planning on downloading the pep.all fasta files.
> 
>  
> Alternatively, after reading various posts on the Maker google group, I realize that I can also download proteomes from teleost fish from UniProt (www.uniprot.org/proteomes <http://www.uniprot.org/proteomes>). UniProt proteomes can contain both reviewed and unreviewed protein sequences and for the fish species I’m interested in downloading, they mostly contain unreviewed proteins.
> 
>  
> Do you recommend that I use the UniProt proteomes instead of the Ensembl proteomes?
> 
>  
> Also, there are actually four different model teleost species with available proteomes that are equally related to my teleost species. They’re all in different taxonomic orders, but that’s as closely related as I can get! Should I stick to just using proteomes from two species or should I up it to three or four?
> 
>  
> In addition, I have read in previous posts that you recommend using a comprehensive set of proteins from UniProt/Swissprot. Avoiding the unreviewed, UniProt/tremble datasets, should I download the complete, reviewed set of all UniProt/Swissprot proteins (uniprot_sprot.fasta.gz <>)? Under taxonomic divisions, there seems to be an option to download just vertebrate Uniprot/Swissprot proteins (the uniprot_sprot_vertebrates.dat.gz <> file). This only seems to be available in a .dat file format, but converting a .dat file into a .fasta seems to be possible.
> 
>  
> My apologies if you have already answered these questions in the past. Any help on these points will be greatly appreciated.
> 
>  
> Thank you,
> 
> 
> 
> Allison
> 
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