A way to align sequences up to 1 Kb

Francois JEANMOUGIN pingouin at crystal.u-strasbg.fr
Thu Jun 5 04:51:28 EST 1997


In article <01BC713B.79F2DDA0 at ras13.isol.net.ar>,
	ustavopa at interserver.com.ar (Gustavo Palacios) writes:
> Dear netters:
> 
> I am looking for a way to align a lot of complete genomes sequences of =
> 10 kb. I have the CLUSTAL V program but it says that it cannot align =
> sequences up from 1500 bp. Does anybody know of other way?

	It's my day guys!

	ClustalV is quite old now and the algorithm was improved by
ClustalW and now, the interface ClustalX. The limitation is made
at the compilation step. You can change it but it depends of how
many memory you have.

	Just picked ClustalX, which includes also ClustalW (the text
version) at (available for most platforms):

	ftp://ftp-igbmc.u-strasbg.fr/ClustalX/

	The new version of Clustal include a DNA matrix with transistion/
transversion weights. The DNA alignemnt is the one for which we have
not enough feed-back to be sure that the algorithm is strong enough.
Please send me any correction or improvement you might need.


						Francois.
-- 
Francois Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine)



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