[Bioperl-l] oligos, mRNAs, and genes

T.D. Houfek tdhoufek at unity.ncsu.edu
Thu Feb 5 21:49:52 EST 2004

There are a lot of people around here a lot more qualified to answer,
and I hope someone will correct me if I misinform you (or
if I've misunderstood your question).  

If you're dealing with a eukaryote, I think the method you are hinting
at, effectively tallying which mRNAs were uniquely matched by your
oligos, could run into problems dealing with alternatively-spliced
genes, where there's not a 1:1
relationship between gene and mRNA product.  But I'm not sure what
the incidence of such genes is typically, I think it is just a few
percent of genes.  This shouldn't prevent you from finding "query
sequences with mappings to only one gene", and it certainly won't keep
you from sampling alternatively spliced products, but there might be a
few cases where one gene has more than one query oligo that matches it
(if multiple matched mRNA transcripts are subsequently related to the
activity of one gene). 

If your mRNA's correlated genes are already well characterized in one of
the major databases / formats, you should be able to use
BioPerl to explore the relations between genes and transcripts, but
is that your situation, or are these transcripts of yours somewhat less
well contextually situated?



 T.D. Houfek
 Tobacco Genome Initiative
 NCSU, Raleigh, NC 27606

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