[EMBOSS] NCBI Blast in emboss-explorer

Luke McCarthy lukem at gene.pbi.nrc.ca
Tue Aug 30 05:28:37 UTC 2005

On Mon, 2005-08-29 at 22:20, Ryan Golhar wrote:
> Has anyone tried incorporating NCBI Blast into the emboss-explorer UI?  
> I haven't read the documentation yet on how to incorporate other
> applications into EMBOSS, as I was hoping someone else has already done
> this with BLAST :)

I don't know precisely what else is required to create an EMBOSS wrapper
(a la emma) around an external program, but if your only concern is
EMBOSS explorer, all you have to do is mock up an ACD file with the same
name as the executable (in the same location as the other EMBOSS ACD
files, usually /usr/local/share/EMBOSS/acd/ or something similar) and
make sure the executable is in the EMBOSS explorer PATH (set in the
configuration module, but by default it's the location of the EMBOSS

In the ACD file, the name of each parameter has to be the command line
switch.  For example:

datafile: i [
	required: "y"

outfile: o [
	required: "y"

For best results, you'd have to put the options in appropriate sections,
etc.  The only tricky part I can see is that you'd have to hardcode your
available BLAST databases in the ACD file.

It's entirely possible that someone has already done this, or has
written an actual EMBOSS wrapper for BLAST.  If there is no such
response forthcoming, I'll whip up a blastall.acd later this week and
put it up on the EMBOSS explorer website.  It would be a good way to
showcase the flexibility of the interface and the ACD language itself.



More information about the EMBOSS mailing list