[BiO BB] blast graphical result & gapped alignment

Mike Marchywka marchywka at hotmail.com
Wed Dec 5 13:41:59 EST 2007

> I am developing a webserver using the standalone BLAST program. I am getting the results. I want to include the graphical results in the text result page(html). How do i go about it? Should i use any GD modules from PERL? And also, i am able to get only the ungapped results, but not the gapped results. though i have included the command -g T -G 13 -E 3. Please let me know how to do gapped alignment.

One option would be to use a servlet to generate html
or use various command line utilities to generate image files that could be displayed with
static or almost static html. It is probably not hard with something like cold fusion but you can get a servlet engine for free :) I haven't used the GD modules but Java provides a lot of simple drawing methods, it is probably
just as fast as PERL and would integrate nicely with servlets. One of the popular genome browsers,
IGB, I think is written in java- you may be able to get source code and


If you are looking for a canned example, you may try contacting sites that do something
similar or just look at their source code- you can probably figure out how they do it.
The coarse graphics I've encountered for viewing sequences look like it is all generated 
html rather than drawn images. 
If you find something you like it is easier to talk about specifics. 
Obviously, a lot would depend on how much customization you think you will need
and performance issues. 

I haven't checked all the available output options but I wrote some bash scripts for reformatting
default blast output into "annotation format" that I use with my own tools. 
If you care to comment on this I would appreciate any input ( click on qseg.bmp to
see the graphics stuff , I'm still putting this together please don't critique web page design :) 
Thanks to phluant.com for providing the server):


The above was generated with C++ tools- quite fast but the bmp files are huge and
don't compress well as jpg. You will probably need to view it in an image viewer rather than browser
as you really will need to zoom in to see details.


Mike Marchywka
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