[maker-devel] Maker question

[Carson Holt]

MAKER will only use NCBI or UniProt if you supply the database.  NCBI provides there databases via ftp, or you can use the NCBI search feature on their website and select your output format to be fasta.  UniProt also provides their database for download.  I suggest using UniProt/Swiss-Prot and not TrEMBL.

Carson

On 10/20/09 3:22 PM, "Daniel Standage" <byuhobbes at gmail.com> wrote:

PS Another quick question. I always assumed Maker used BLAST only for internal sequence comparison. Maker doesn't BLAST against NCBI or Uniprot or anything like that does it?

On Tue, Oct 20, 2009 at 3:20 PM, Daniel Standage <byuhobbes at gmail.com> wrote:
Carson,

I was going to send this to the mailing list, but Chris Conley said it would probably be fine if I sent it directly to you. Thanks for your help so far.

We're getting ready to use maker for annotating a fungal genome. I feel like I have a pretty good understanding of what goes into and comes out of maker (thanks to the summer school session and some time on my own playing with it). However, it's not clear to me how to integrate available data from a model organism. I feel like if we just toss everything into the mix, maker won't differentiate between organism we're studying and the organism we're using as a reference.

Is it possible to use data from a closely related organism to assist maker? If so, do we just toss the data into the mix or do we need to indicate that the data is from a reference organism? There is genomic, transcriptomic, and proteomic data available, and it would probably go a long way to improve any gene models maker predicts.

Thanks.

Daniel Standage
Plant Genetics Lab
Brigham Young University


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