[Gmod-help] RE: [Gmod-gbrowse] Displaying protein residues using the segments glyph

[Remo Stierli]

Hi Dave,

I have tried the translation glyph, but I cannot get the desired output.
I would like to translate the sequence associated with the feature. The
translation, however, seems to be based on the reference sequence. 
Even ought the translation glyth is set to "1frame" three frames are drawn
(when zoomed in and zoomed out). 
In addition, the translation is not aligned. It shows always the very
beginning of the translation (does not slide with the window).


[Polypeptide]
feature      = polypeptide:prot4EST
glyph        = translation 
frame0       = darkred
height       = 10
fgcolor      = blue
strand	 = +1
translation  = 1frame
category     = Proteins
key          = Polypeptide
link 		 = AUTO
link_target	 = _blank

Many thanks,
Remo

-----Original Message-----
From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com] 
Sent: Dienstag, 7. Oktober 2008 16:12
To: Remo Stierli
Cc: Gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] Displaying protein residues using the segments
glyph

Remo,

According to
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Gl
yph/segments.html:

  There is also a -draw_protein_target option, which is designed for
  protein to nucleotide alignments. It draws the target sequence every
  third base pair and is supposed to align correctly with the forward
  and reverse translation glyphs. This option is experimental at the
  moment, and may not work correctly, to use with care.

This option was added 2 years ago by Lincoln (see
http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=10641)
but it does not appear to have seen much, if any, use since then.

Another option is to try the translation glyph.  It has a "1frame"
translation that might do what you are looking for (although I have
not tried that either).

Dave C
GMOD Help Desk

On Wed, Oct 1, 2008 at 11:53 AM, Remo Stierli <rstierli at gmx.ch> wrote:
>
> What is the proper configuration of the segments glyph in order to display
> the protein residues?
> On the test data below, the -draw_dna and -draw_target switches seem to
work
> (drawing glyph & sequence). However if the -draw_protein_target option is
> selected only the glyph is spawned (sequence not displayed).
>
> Remo Stierli
>
>
> Sample:
> =================================================================
> [polypeptide]
> feature      = polypeptide
> glyph        = segments         #$Id: segments.pm 14687 2008-05-29
14:17:43Z
> lstein $
> draw_protein_target     = 1
> strand_arrow = 1
> category     = Proteins
> key          = Polypeptide
> link             = AUTO
> link_target      = _blank
>
>
>
> ##gff-version   3
> ##sequence-region   YY_Bb7130AaEcon4641 1 1344
> YY_Bb7130AaEcon4641     phrap   contig  1       1344    .       +       .
> ID=YY_Bb7130AaEcon4641;Name=YY_Bb7130AaEcon4641
>
> YY_Bb7130AaEcon4641     prot4EST        polypeptide     1       1344    .
> +       2       ID=YY_Bb7130AaApep4641;Target=YY_Bb7130AaApep4641 1
>
317;Name=YY_Bb7130AaApep4641;conf_end=716;conf_start=150;ext_end=956;ext_sta
>
rt=3;gene_location=nuclear-encoded;method=similarity;start_frame=3;Target=YY
> _Bb7130AaAgen4641 1 1344
>
>
>
>
> ##FASTA
>>YY_Bb7130AaEcon4641
> TTATGTATGTGAAGTGTTGATGCGTAGTGGCCGGGTCCCTGGTTGATCCTGCCAGTAGTT
> ATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTGCAAGCCGTATTAAGGCGATA
> CCGCGAATGGCTCAATATATCAGTTTTGGTTCCTTAGATCTTACTCGGTTACTTGGATAA
> CTGTGGTAATTCTAGAGCTAATACATGCAATCAGAACTCTGACCAGTGATGGGATGAGTG
> CTTTTATTAGATCAAAACCAATCGACGGAGGGCCTCGCGTCCGAAGTCGTTAATTTTTGA
> TGAATCTGGATAACTTTTGCCGATCGCATGGTCCAGTACCGGCGACGCATCTTTCAAATG
> TCTGCCTTATCAACTTTCGATGGTAGTTTCTGCGACTACCATGGTTGTCACGGGTAACGG
> GGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGG
> CAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATA
> CGGGACTCTTACGAGGCCTCGTAATCGGAATGAGTACACTTTAAATATTTTAACGAGGAA
> CAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATAC
> TAAAATTGTTGCGGTTAAAAAAGCTCGTAGTTGCATTTGTGCGCCGCGCTGTCGGTGCAC
> CGCATCCGCGGTGATACTGACACGTCTGCGGAGCATATCGTCGGTGAGCCGGCGTTGTAA
> CAAACGTCGGTTCAATATCAAAATCCTATCGCGGTGCTCTTCGGTGAGTGTCGAGATGGG
> CCGACAATTTTACTTTGAACAAATTAGAGTGCTCAAAGCGGGCTCAAAATGCTGCTTGAA
> TATTTCGTGCATGGAATAATAGAATATGATCTCGGTTCTATTTTGTTGGTTTTCAGAACT
> CCGAGGTAATGATTAATAGGGATAACTGGGGGCATTCGTATTGCGACGTTAGAGGTGAAA
> TTCTTGGATCGTCGCAAGACGAACATCAGCGAAAGCATTTGCCAAAGGTGTTTTCATCAA
> TCAAGAACGAAAGTTAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTAACCGTAAA
> TATGTCATCTAGCGATCCGCCGACGTTACTACAATGGCTCGGCGGGCAGCTTCCGGGAAA
> CCAAAGATTTTGGACTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGAC
> GGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAATCTCA
> CCAGGCCCGGACACCGGAAGGATTG
>>YY_Bb7130AaAgen4641
> AAAAAAAAAAAAAAAAAAAATGCGTAGTGGCCGGGTCCCTGGTTGATCCTGCCAGTAGTT
> ATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTCAGTGCAAGCCGTATTAAGGCGATA
> CCGCGAATGGCTCAATATATCAGTTTTGGTTCCTTAGATCTTACTCGGTTACTTGGATAA
> CTGTGGTAATTCTAGAGCTAATACATGCAATCAGAACTCTGACCAGTGATGGGATGAGTG
> CTTTTATTAGATCAAAACCAATCGACGGAGGGCCTCGCGTCCGAAGTCGTTAATTTTTGA
> TGAATCTGGATAACTTTTGCCGATCGCATGGTCCAGTACCGGCGACGCATCTTTCAAATG
> TCTGCCTTATCAACTTTCGATGGTAGTTTCTGCGACTACCATGGTTGTCACGGGTAACGG
> GGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGG
> CAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATA
> CGGGACTCTTACGAGGCCTCGTAATCGGAATGAGTACACTTTAAATATTTTAACGAGGAA
> CAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATAC
> TAAAATTGTTGCGGTTAAAAAAGCTCGTAGTTGCATTTGTGCGCCGCGCTGTCGGTGCAC
> CGCATCCGCGGTGATACTGACACGTCTGCGGAGCATATCGTCGGTGAGCCGGCGTTGTAA
> CAAACGTCGGTTCAATATCAAAATCCTATCGCGGTGCTCTTCGGTGAGTGTCGAGATGGG
> CCGACAATTTTACTTTGAACAAATTAGAGTGCTCAAAGCGGGCTCAAAATGCTGCTTGAA
> TATTTCGTGCATGGAATAATAGAATATGATCTCGGTTCTATTTTGTTGGTTTTCAGAACT
> CCGAGGTAATGATTAATAGGGATAACTGGGGGCATTCGTATTGCGACGTTAGAGGTGAAA
> TTCTTGGATCGTCGCAAGACGAACATCAGCGAAAGCATTTGCCAAAGGTGTTTTCATCAA
> TCAAGAACGAAAGTTAGAGGTTCGAAGGCGATTAGATACCGCCCTAGTTCTAACCGTAAA
> TATGTCATCTAGCGATCCGCCGACGTTACTACAATGGCTCGGCGGGCAGCTTCCGGGAAA
> CCAAAGATTTTGGACTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGAC
> GGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAATCTCA
> CCAGGCCCGGACACCGGAAGGATTG
>
>
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