I am just getting familiar with one of the many packaged that do this kind of prediction because I need  to figure out the implemented scoring logic. 
The package uses three steps for targets selection. Namely:
- sequence complementarity using a position-weighted local alignment algorithm
- free energies of RNA-RNA duplexes
- conservation of target sites in related genomes

The energy minimization algorithm looks wierd to me. 
I don't quite get the other two phases. I was hoping something similar can be reproduced using Biomart functions
to the purpose of understanding the package scoring criteria. After all, it looks like a sequence alignment problem ... 

Thank you,
Maura

-----Messaggio originale-----
Da: Sean Davis [mailto:seandavi@gmail.com]
Inviato: dom 09/08/2009 19.36
A: mauede@alice.it
Cc: Bioconductor List
Oggetto: Re: [BioC] Pairwise Sequence Alignments
 
On Sun, Aug 9, 2009 at 10:15 AM, <mauede@alice.it> wrote:

> I am browsing through the Biostring on-line docu,mentation. I wonder
> whether the illustarted techniques (functions) for Pairwise Sequence
> Alignments are being usd in any of the packages aimed at predicting miRNA
> target-genes match.
> I only haveonly used miRANDA which makes us of the Smith-Waterman
> algorithm. However I cannot recognize any of Biostring techniques for
> sequence alignment. I may be confused by the lack of documentation &
> comments in miRANDA C code.
> Thank you in advance,
>

Hi, Maura.  This not an answer to your question, but miRNA target prediction
is not just a function of pairwise alignment and is a research field unto
itself (and not a field I am closely aligned with), so your best bet is to
use published algorithms and predictions unless you have a specific need to
improve on existing techniques (which implies understanding every detail of
what they do).

Sean







tutti i telefonini TIM!


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