[Bioperl-l] How to produce Bio::Graphics images using PROSITE output ?

Shameer Khadar shameer at ncbs.res.in
Tue May 15 03:03:57 UTC 2007

Dear All,

Thanks a lot for all your inputs [Help : Imagemaps using Bio::Graphics ].
I am still working on the other part of this project. Now, I am sure that
I can impliment it using Bio::Graphics. I will come back to imagemaps with
in a week or two.

Meanwhile, I need to parse a prosite output to present it as a
Bio::Graphics image. Any one had tries Bio::Graphics to create images
using prosite output ? I tried in the How-to I couldnt find anything
related to prosite.

My output looks like this :
    >Sequence : PS00001 ASN_GLYCOSYLATION N-glycosylation site.
          75 - 78  NGSM
    >Sequence : PS00005 PKC_PHOSPHO_SITE Protein kinase C phosphorylation
         41 - 43  SpK
    >Sequence : PS00008 MYRISTYL N-myristoylation site.
           6 - 11  GTitNQ
    >Sequence : PS00009 AMIDATION Amidation site.
          78 - 81  mGKR

I need to impliment an image like blast-parser image.
Thanks to any inputs/pointers.

> The width of the image is determined by the -width attribute and is given
> in
> pixels. You cannot control the height of the image as it is computed
> dynamically based on the number of features and bumping options.
> Lincoln
> On 5/1/07, Shameer Khadar <shameer at ncbs.res.in> wrote:
>> Dear Scot,
>> > There is a fair amount of documentation in the perldoc for
>> > Bio::Graphics::Panel under the section called 'Creating Imagemaps';
>> have
>> > you read that?
>> I agreed, but I couldnt the exact information I needed :( (may be I
>> missed
>> something important).
>> >  Also, for changing the scale, that should happen
>> > automatically--have you tried yet?
>> I tried by changing the Lincoln's program eg: blast3.pl
>> my $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>1000);
>> to my
>> $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>300);
>> But it had given me a smaller scale of length upto 300. I was looking
>> for
>> an option where I need same width and height of given image and a
>> dynamic
>> start and end values depending on length of my sequence. Since I couldnt
>> accomplish, I thought of getting some help from you guys. I think I need
>> to play a little bit with the value for reformat the scale to accomodate
>> my hits as well.
>> Thanks a lot for your inputs,
>> --
>> Shameer Khadar

Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in

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