[InterMine Dev] AIC (Alternative Initiation Codon) mapping as a function in Intermine

davies d.s. (dsd2g13) dsd2g13 at soton.ac.uk
Thu Feb 18 21:04:45 GMT 2016


I need to make Intermine map arbitrarily found sequences of three letters to text files of DNA code, that is, I need it to find them in the text files at specific locations, and I need it to take the text in the particular paragraph after the spot where it has found them, stick it to the beginning of the next paragraph minus the paragraph's title, and spit the results out in another text file.
Not only that, but I need it to pick the three letter codons based on certain parameters.
I need it to do this however many times is necessary per gene for a whole list of genes
where 'however many times is necessary' is determined by how many criteria-fitting codons there are per gene.
The resultant text should be displayed on the web page too and it should be available for follow-up queries. However, at the moment I can't even get it to display any of the data it has.
www.intermine.org and intermine.readthedocs.org have sort of helped but I need more brains to throw at this than fit in my head tonight. My deadline to at least know how to do this is Saturday, sorry it's a bit short notice but it is part of my third year dissertation as well as a longer term project for Vulpine Designs Unlimited.


Daniel Davies
Third year student, BSc Biochemistry

Founder,
The Dorset Constructorium
http://www.constructorium.org

Founder & CEO,
Vulpine Designs Unlimited
http://www.vulpinedesigns.co.uk
Freedom of Form: an evolution revolution
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