发信人: LecEgf (no+sugar), 信区: Biology
标 题: This may be useful for you!: ClustalW
发信站: Unknown Space - 未名空间 (Tue Oct 14 00:54:25 2003) WWW-POST
http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/help8.html
A new matrix can be read from a file on disk, if the filename consists only of
lower case characters. The values in the new weight matrix must be integers
and the scores should be similarities. You can use negative as well as
positive values if you wish, although the matrix will be automatically
adjusted to all positive scores.
【 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?
: : : :
: : : :
: : : :
: : :
: : :
: :
: :
:
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