jason zhang wrote:
With regards to -sprotein/-snucleotide for antigenic, the web interface
can not tell that since there is no such information in ACD. I expect
the end user has some basic knowledge about the program and will not
make such mistake.
Indeed, it is often best to trust the users.
The information is in ACD, but it is in the sequence "type" which you
would have to interpret as nucleotide, protein, or both.
Some ACD files that allow both types also use a variable "ACDPROTEIN"
that is set to the type of the first sequence - this allows you to make
protein or nucleotide specific versions with appropriate default values
- the alignment progams are common examples of this.
Not all information in ACD is used. Some information such as variable,
pattern can not be easily translated to javascript in web page. Again, I
expect the end user can work it out. Otherwise error will occur at
execution time.
We try to avoid these. If you run "acdvalid <progamname>" you may see
warnings for things that can be difficult for parsers. Let us know if
any of these give you major problems - or if there are problems we fail
to detect. We try to reduce the number of acdvalid warnings for all
emboss applications before each release.
regards,
Peter
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