[BiO BB] blast graphical result & gapped alignment

[Carlos Viana]

You could use GBrowse for display your results. You may include graphical
results using tracks for each type of results: gapped and ungapped. For
details and examples:

* Details
http://www.gmod.org/wiki/index.php/Gbrowse#Documentation
http://www.bioperl.org/wiki/Gbrowse

* Examples
http://www.hapmap.org/cgi-perl/gbrowse/hapmap_B35/?name=Chr20
http://flybase.net/cgi-bin/gbrowse/dmel/


Carlos Juliano.


On Dec 5, 2007 4:27 PM, Ryan Golhar <golharam at umdnj.edu> wrote:

> 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
> > 586 Saint James Walk
> > Marietta GA 30067-7165
> > 404-788-1216 (C)<- leave message
> > 989-348-4796 (P)<- emergency only
> > marchywka at hotmail.com
> > Note: Hotmail is blocking my mom's entire
> > ISP claiming it is to reduce spam but probably
> > to force users to use hotmail. Please DON'T
> > assume I am ignoring you and try
> > me on marchywka at yahoo.com if no reply
> > here. Thanks.
> >
> >
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-- 
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* Carlos Juliano
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