[NORDNS] [Bioperl-l] matching miRNAs to one or a lot of mRNAs

[Brian Osborne]

Starr,

Bioperl has some good tools for the blastn searches that you're suggesting.
So if you'd like to explore the "text matching" approach then Bioperl could
facilitate this, yes.

Bioperl can also run EMBOSS programs like dan, which calculates or predicts
the Tm for a given DNA or RNA. The only fly in the ointment may be that you
cannot specify a specific pair of RNAs in dan, you seem to be only be able
to specify % mismatch given one RNA duplex- perhaps this isn't exact enough.
Go to www.emboss.org to learn more about the dan program. So the idea might
be to find related sequences using blastn, find their % percent mismatch,
then use dan.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Starr Hazard
Sent: Friday, September 26, 2003 2:30 PM
To: bioperl-l at bioperl.org
Subject: [NORDNS] [Bioperl-l] matching miRNAs to one or a lot of mRNAs

Folks,

In a recent paper, Kawasacki et al(pubmed 12808467) report on the
interaction between a specific miRNA (human miRNA23 g.i. 17646028) and a
specific mRNA (human HES1 g.i. 8400709). They suggest they did a BLAST
search and ultimately located the interaction. I cannot duplicate their
data mining and cannot find the association they describe.

In general, is there a way to take a library of miRNAs and evaluate their
potential interaction with a particular mRNA? Or is there a data mining
tool that could screen a large pool of mRNAs for
significant interactions with a pool miRNAs?

I cannot at present see any BioPerl tools that address this issue (right
now that means I scanned the FAQ for the string RNA and searched the
BioPerl site for RNA but found only some traffic about Seq.pm).The people I
have asked seem divided about whether this is
text matching issue or more of a hybridization issue involving
an energy of interaction evaluation.

Anybody got any pointers to offer?

Starr

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