[EMBOSS] NCBI BLAST under EMBOSS

[Guy Bottu]

	Dear Ryan, dear all,

You can download from http://www.wemboss.org/ wrappers4EMBOSS, which 
allows to access BLAST (as well as some other software) from under EMBOSS 
(as the standard distribution of EMBOSS already does for CLUSTAL and 
Primer3). Note by the way that an article about it appeared in EMBnet.news 
11(1) (see http://www.embnet.org/download/embnetnews/). Some further 
remarks :

- Just putting the blastall program in the EMBOSS .../bin directory and 
writing a blastall.acd file will not work well (only fastA format query 
sequence accepted, need to write absolute path to databanks in ACD file 
since the Web interface has no BLASTDB shell environment variable, etc.). 
Better is to write an EMBOSS "wrapper" program that starts by reading the 
ACD file and does whatever else is needed. Our "wrapper" can, among other 
things, generate on-the-fly from a List of sequences a databank to be 
searched.

- Our "wrapper" works well in a terminal and under wEMBOSS. Since the ACD 
syntax is quite complex it does not run well under all GUI's. I know that 
the old EMBOSS-GUI of Luke did not manage well the hide/unhide of 
the parameters. I do not know how EMBOSS Explorer works ; I would like to 
hear about it as soon as somebody tested. To make BLAST work under all 
GUI's it might, as proposed, be needed to make separate programs for 
blastn, blastp, etc.

- The databanks are indeed a problem. An EMBOSS library module that can 
find the databanks (as exists in GCG) would be nice. In the mean time, our 
wrappers need the databank names in the ACD files. As you will see if you 
try, wrappers4EMBOSS asks for the names of the databanks when you install 
it. A problem is that whenever you change the collection of databanks on 
your site you need to do the installation again or edit manually the ACD 
files.

	Hope this helps,
	Guy Bottu,
	Belgian EMBnet Node