[Bioperl-l] In silico Chromosome Walking

[Razi Khaja]

Hello Ferdi,
There is a software called PartiGene that may do this type analysis.  I
have never used this software but have heard from some of the researchers
here that it is able to construct gene sequences from EST fragments.  If
this is what you are trying to do, you may want to look at
http://www.nematodes.org/PartiGene/
Hope that helps.
Razi 


--- Ferdinand Marletaz <ferdinand.marletaz at gmail.com> wrote:

> Hi,
> 
> I'd like to find a script to make a kind of chromosome walking in  
> matching pieces of cDNA on Traces of a Genome in order to find whole  
> gene sequence from a little degenerate PCR fragment (100-500 pb).   
> I've heard about  GenoTrace but it seems impossible to get it on the  
> internet (link doesn't work http://rat.niob.knaw.nl/GENOTRACE/)  and  
> I haven't understood if it requires full length cDNA or if it can  
> work with shorter sequences (it would be possible to run GenScan on  
> the previously obtained contig...)
> 
> Does anybody have the source of GenoTrace or an idea for my problem.
> 
> Thank you very much
> 
> Ferdi
> 
> 
> 
> 
> 
> ___________________________________________
> Ferdinand Marlétaz
> Structure and Evolution of Nuclear Hormone Receptors
> Laboratoire de Biologie Moléculaire de la Cellule (UMR 5161)
> Ecole Normale Supérieure de Lyon
> 46, Allée d'Italie
> 69364 Lyon Cedex 07,  France
> Tel. (33) 04 72 72 82 85
> Port. 33 (0)6 30 35 58 49
> Fax. (33) 04 72 72 80 80
> Mail. Ferdinand.Marletaz at ens-lyon.fr
> 
> 
> 
> 
> 
> 
> 
> 
> 
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/**
 * Razi Khaja, Bioinformatics Analyst
 * The Hospital for Sick Children, Toronto
 * The Centre for Applied Genomics, www.tcag.ca
 * Tel 416-813-7032, Fax 416-813-8319
 */