[BiO BB] blast graphical result & gapped alignment

Ryan Golhar golharam at umdnj.edu
Wed Dec 5 15:27:27 EST 2007

BioPerl has an example of creating a graphic from Blast output.

Mike Marchywka wrote:
>> 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
> adapt:
> http://www.affymetrix.com/support/developer/tools/affytools.affx
> 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):
> http://www.spottext.com/marchywka/mydownloads.cfm
> 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.
> Thanks.
> Mike Marchywka
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