Dear Nathaniel,

My name is Junjun Zhang, I work on the BioMart project. I am happy to assist 
you in building a biomart db.

To start off, I need to know more about what you have and what you wish to 
achieve. Could you email me (off the mailing list) some example files of the 
following items you mentioned earlier?

> What I want is to know how to go from a starting point of 
> having a)genomic, transcript and protein FASTA files b)a GFF3 
> file for transcripts c)a table of gene annotation information 
> to setting up BioMart.

Thanks,
Junjun



> -----Original Message-----
> From: [email protected] 
> [mailto:[email protected]] On Behalf Of Nathaniel Street
> Sent: Friday, February 19, 2010 2:27 AM
> To: [email protected]
> Subject: [mart-dev] Documentation request
> 
> Hi
> 
> We are setting up a web resource for a draft genome. We have 
> GBrowse up and running no problem but now want the same data 
> (sequence and basic
> annotation) to be available via BioMart. I am not a 
> computer/bioinformatics 'expert'. I'm a biologist learning to 
> use computers so I am at the hands of the quality of 
> available documentation for resources. Pointing me to an 
> existing Mart doesn't really help me know how to go from a 
> starting point of nothing to a working Mart.
> 
> I have searched the mailing list for anything relevant I can 
> think of. I have even found *identical* requests to this one 
> but nothing has come of those posts (other than 'look at one 
> of our existing ensembl marts').
> 
> What I want is to know how to go from a starting point of 
> having a)genomic, transcript and protein FASTA files b)a GFF3 
> file for transcripts c)a table of gene annotation information 
> to setting up BioMart. I imagine this has to be a common task 
> so I am surprised there is no documentation on this. As part 
> of the GMOD project it would be great to see an integrated 
> tutorial on setting up GBrowse and getting the same data into 
> a working Mart.
> 
> I have looked at and tried to use the gff2biomart script 
> (various versions of it) but after much effort got nowhere. I 
> have also asked someone far more familiar with mysql and perl 
> to have a go. They got a lot further than me but still not to 
> a working Mart. We both managed to get simple tables 
> structures for location and annotation information working 
> but the sequence side of things is a complete mystery.
> 
> So, is there any documentation available and if not can 
> anyone help me go from FASTA+GFF3+annotation table to a 
> working Mart? If someone can help I am more than willing to 
> write up the end process into a walk-through guide so that 
> others benefit.
> 
> Thanks
> 
> Nathaniel
> --
> Nathaniel Street
> Umeå Plant Science Centre
> Department of Plant Physiology
> University of Umeå
> SE-901 87 Umeå
> SWEDEN
> 
> email: [email protected]
> tel: +46-90-786 5473
> fax:  +46-90-786 6676
> 
> www.popgenie.org
> 

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