Re: Maker running with tRNAScan and Interpro

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Re: Maker running with tRNAScan and Interpro

Carson Hinton Holt
Re: Maker running with tRNAScan and Interpro There is currently not an easy way to integrate tRNAScan, but there is for interproscan.  There is an ipr_update_gff and a iprscan2gff3 script which will turn interproscan raw format output into GFF3 visible features and tag genes with corresponding domain information.  Make sure to run iprscan with --iprlookup the goterms option and raw format all turned on.  Run iprscan against the MAKER proteins fasta files only.

If you have more questions, let me know.  I may be a little slow because I just moved to Toronto (still don’t have internet at home), and I start at my new lab on Monday.

Check the MAKER download page to see what the current version of MAKER is compared to yours.  There will be more updates soon, when I finally get everything with my move calmed down.


On 7/14/11 9:33 AM, "Filipe Bregieiro" <filipegoncalo.duarte@...> wrote:

Hi Mr Carson,

How have you been doing? Hope everything is ok with you!
I am writing to ask you something, is it possible to integrate tRNAScan and interpro into Maker, so that the maker's produced .gff file will also include info from these two predictors?
And also, how can i make sure that my maker is up-to-date, and if not, how can i update it? Is there any "easy" way?


PS: My work is almost done, and from a sequence.fasta, i can now produce  the gff file, include it into my chado database, and visualize data with gbrowse and/or artemis. So, soon i will start my writing my repor, and i would like to know if i could include your name in the acknowledgements part of it. I asked the same thing to Mr.Scott. I would like to do this, because you were trully, a precious help for me, in order to achieve the goals i was asked for.

Carson Holt
Graduate Student
Yandell Lab
Eccles Institute of Human Genetics
University of Utah

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