[Bioperl-l] Mapping Blast results

[Scott Cain]

Hi Shalabh,

Please keep your responses on the list.

A few things:

* While it interesting that the resulting png isn't readable (and I
don't know why--perhaps the script is silently crashing?), I have to
wonder if a graphic with 1500 hits for a particular gene will be of
that much use anyway?  Perhaps, but it seems to me that 500 will do
just as well as 1500 :-)

* When you say you don't know how to map hits to a particular gene,
what is the hang up?  Coordinate mapping?  Converting blast results to
GFF?

Scott


On Tue, Feb 2, 2010 at 1:47 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi,
>      thanks for your quick reply.
> Actually i am getting a png file but its not readable (there are about 1500
> hits).
> I have a working Gbrowse on my system but i don't know how i can map my
> blast reads to a particular gene.
> Thanks
> Shalabh
>
> On Tue, Feb 2, 2010 at 1:34 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Shalabh,
>>
>> When you say it's not working, what do you mean?  Presumably, you
>> could write a script that uses Bio::DB::SeqFeature::Store if speed is
>> the problem, but if you wanted to go that far, your time would
>> probably be better spent installing GBrowse.
>>
>> Scott
>>
>>
>> On Tue, Feb 2, 2010 at 10:16 AM, shalabh sharma
>> <shalabh.sharma7 at gmail.com> wrote:
>> > Hi,
>> >    I am trying to map blast results on a gene. I am using Bio::Graphics
>> >    http://bioperl.org/wiki/HOWTO:Graphics
>> >
>> > This is working fine for small blast files but not for large blast file
>> > with
>> > lot of hits. Is there any way i can use this for large blast files?
>> >
>> > Thanks
>> > Shalabh
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research