a www site to run DNA/protein sequence analysis programs

Shiping Zhang ping at bnlux1.bnl.gov
Mon Aug 14 09:51:36 EST 1995


In article <40ipr9$4lh at sun20.ccd.bnl.gov>,
Shiping Zhang <ping at genome1.bio.bnl.gov> wrote:
>Those who want to do some simple DNA/protein sequence analysis
>but don't have a program at hand can take a look at the www site
>
>http://genome1.bio.bnl.gov/bbq.html
>
>At the moment, there are several dozens of programs available doing
>DNA/protein sequence analysis, such as pI calculation, restriction
>enzyme analysis, oligo Tm/dG calculation, sequence comparison, GenBank
>data retrieval, etc.

We fixed a bug with fasta setup.  Due to the bug, the result was not
sent back to the user.  If you have run fasta through BBQ and didn't
get anything, you may try again.

Those who have tried BBQ would probably feel that the biggest problem
is inputting sequence data.  Though the cut/paste feature likely exists
in your browser, it's realy not as convenient as simply typing a file
name (along with the path if necessary).  We have proposed to add
a new tag to the fill-out FORM so the input to a field marked with
the tag will be taken as a local file name and the content of the file
will be loaded by the browser as the real input when the form is submitted.
As a test, I have modified lynx2-3-7 to recognize such a tag and do as
specified above and it works really great.  It really needs little
effort to add such a feature into a browser.  The IETF group for HTML has
extented the specs to include such a tag.  But it tries to cover a lot
of situations, such as binary data (therefore involving encode/decode and
type specification for different binary format, such as .tiff, .gif, .wav,
.au, etc), and makes it very very complicated to implement the tag.  So far,
I'm not aware of any browser that has implemented the IETF tag. (Some
browsers may allow you to directly upload the content of local files into
a field.) To sort of working around such problem, we implemented a mechanism
in BBQ that allows you to input a sequence only once for repeatly uses.
(See "sequence input method" and "retain" at above www site for details.)

-ping





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