[Bioperl-l] Graphical alignments with blast

[Steven Lembark]

-- Jason Stajich <jason at cgt.duhs.duke.edu>

> On Tue, 16 Dec 2003, Mike Muratet wrote:
>
>> Greetings
>>
>> I am trying to roll my own simple graphical alignment from blast data
>> (unless of course someone already knows of one). As near as I can figure
>> from bptutorial and the man pages, the approach would be create a set of
>> LocatableSeq objects to manually create a SimpleAlign object. At that
>> point,

You can also look at non-alignment graphical viewers
such as the w-curve (see bioinfo.org for example code).
The curve-based tools use some sort of state machine
to generate a trace of the DNA, which then becomes the
curve used for testing similarity. We've had good luck
with variations on the w-curve so far at IIT.


--
Steven Lembark                               2930 W. Palmer
Workhorse Computing                       Chicago, IL 60647
                                            +1 888 359 3508