[EMBOSS] siRNA improvements

[Gary Williams, Tel 01223 494522]

Thanks for the suggestions.
I'll take a look.
Gary

Stefanie Lager wrote:
> 
> Hi,
> 
> It would be nice if the EMBOSS application sirna could incorporate
> simple calculation of free energy, to improve the siRNA design. Lately
> several reports on siRNA design (reviewed in Silva et al 2003) have
> showed the importance of making the 5' end of the antisense strand
> less stable than the 3' end (Schwarz et al 2003). Also the center part
> should show a lower internal stability (Khvorova et al 2003). Simple
> energy profiles can be calculated by the method of Mathews et al
> (Mathews et al 1999). Several of the commercial siRNA design servers
> have already incorporated free energy parameters in the design, and it
> would really be nice to have an alternative.
> 
> Stefanie
> 
> Silva JM, Sachidanandam R, Hannon GJ.
> Free energy lights the path toward more effective RNAi
> Nat. Genet. 2003, 35:303-305.
> 
> Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD.
> Asymmetry in the assembly of the RNAi enzyme complex.
> Cell. 2003 115:199-208.
> 
> Khvorova A, Reynolds A, Jayasena SD.
> Functional siRNAs and miRNAs exhibit strand bias.
> Cell. 2003 115:209-216.
> 
> Mathews DH, Sabina J, Zuker M, Turner DH.
> Expanded sequence dependence of thermodynamic parameters improves
> prediction of RNA secondary structure.
> J Mol Biol. 1999 288:911-940.
> 
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-- 
Gary Williams	MRC Rosalind Franklin Centre for Genomics Research
		Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
		Tel: +44 1223 494500		Fax: +44 1223 494512
		E-mail: name at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk