Re: ClustalW help-NEED EXPERTS! - 未名空间MITBBS历史存档

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Re: ClustalW help-NEED EXPERTS!

Re: ClustalW help-NEED EXPERTS!# Biology - 生物学

f*j2003-10-14 07:10

1 楼

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

y*u2003-10-14 07:10

2 楼

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!

in
nucleotide
are
and
line)?

【在 f***j 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

h*b2003-10-14 07:10

3 楼

in
nucleotide
do you mean sth like this?
clustalw input.aln -gapopen=8.0
what software are you using? PC DOS stand alone clustalw or GCG? Unix or
windows? I am no expert, but I think this not that difficult, if you have an
ansi c compiler, I am sure you can do this easily.
For example, all parameters(like listed partially below):
*********************
/*
multiple alignment parameters
*/
float dna_gap_open = 15.0, dna_gap_extend = 6.66;
float prot_gap_open = 10.0, prot_gap_extend = 0.2;

【在 f***j 的大作中提到】