发信人: yyliu (bonzo), 信区: Biology
标 题: Re: ClustalW help-NEED EXPERTS!
发信站: Unknown Space - 未名空间 (Tue Oct 14 00:42:13 2003) WWW-POST


what kind of sequences are they? DNA or Protein? I guess they are protein
sequences, since you are using CLUSTALW / T-coffee?

I am not familiar with CLUSTALW, since I don't use it. But I do know several
other alignment programs that give better results than CLUSTALW. Or if you
really want to use CLUSTALW, I may be able to look at the program and help you
figure it out.

You can email me for more details.

Good luck!

【 在 feizj (cornell) 的大作中提到: 】
: 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?
: : : :
: : : :
: : : :
: : :
: : :
: :
: :
:
:


--
※ 来源:．Unknown Space - 未名空间 mitbbs.com．[FROM: 171.65.]