[Bioperl-l] In silico Chromosome Walking

Cook, Malcolm MEC at Stowers-Institute.org
Tue Sep 13 17:38:44 EDT 2005


You might email Edwin Cuppen <ecuppen at niob.knaw.nl> (cc:ed) for help with genotrace installs.  I have locally installed genotrace using distribs he provided me.  He was also willing to add my favorite organism du jour (Sea Urchin) to the list of organisms when i asked him nicely (back in August '04 when it mattered)....

Earlier he wrote me:

	Attached is genotrace distrib file. It contains both versions 1 and 2. V1 is 
	not supported anymore but well-documented. It is suitable for stand-alone 
	installation. Version 2 is a web version that uses sanger ssaha server. 
	Currently, there is no documentation for v2, so you'll have to figure out how 
	to use it by yourself. Some quick tips: 
	-There are differences in how traces are stored in v1. and v2. You need MySQL 
	for v2. 
	-Put files from "bin" directory to e.g. "/usr/local/bin/genotrace", and files 
	from "htdocs" directory into your apache tree. 
	-Check scripts in "cgi-bin" and modify $GHOME and $GBIN if necessary. 
	-Check scripts in "bin" directory and modify $mysqluser. 
	-Run genotrace_installDB. 
	-There is a long list of prerequisite software. You'll figure it out in the 

If you don't get a rise from him, email me and I'll forward the (GPL'ed) source to you...

Sorry for the brevity of my earlier response.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Ferdinand Marletaz
Sent: Tuesday, September 13, 2005 4:59 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] In silico Chromosome Walking


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


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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