发信人: feizj (cornell), 信区: Biology
标 题: Re: ClustalW help-NEED EXPERTS!
发信站: Unknown Space - 未名空间 (Tue Oct 14 00:20:02 2003) WWW-POST

I have more than 2,000 groups need to be aligned, that's why I can't use
public web interface (although they have many options but I can get all more
options using command line) but to write shell scripts to run my alignments in
batch. I can't find the options to set score for mismatch and match nucleotide
in several multiple sequence alignment programs such as ClustalW, T-coffee.
The default values (1.9 for match and 0 for mismatch in ClustalW) do not fit
my case.

Desperately need some experts to tell me how to do this? Or let me know any
multiple sequence alignment program which has options for setting gap open
penalty, gap extension penalty, score for mismatch and match nucleotide.


【 在 bigfatliar (Chico Verde) 的大作中提到: 】
: Can't you just go to this website and do all your analysis there? There are
a
: bounch of options.
: http://www.ddbj.nig.ac.jp/E-mail/clustalw-e.html
:
: 【 在 worryless (无忧) 的大作中提到: 】
: : 太专业了，得问major in bioinformatics的人
: : 【 在 feizj (cornell) 的大作中提到: 】
: : : Does anyone know how to set the score for mismatch (negative value) and
: : match
: : : (positive value) nucleotides, respectively, in clustalW (command line)?
: : :
: : : Does anyone know how to make a DNA matrix file for clustalW?
: : :
: : :
: : :
: :
: :
:
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