[Gmod-help] Fwd: a problem about ProteinDumper in GBrowse2.25

[Scott Cain]

Hi Aaron and Xiao Jin,

I'm cc'ing this to the GBrowse mailing list.

I took a quick look, and in the current release of GBrowse (2.33), the
ProteinDumper appears to work at least partially correctly.  That is,
it gets strand info correct and gives the appropriate translation when
the feature is in the negative strand.

What I'm not sure is correct about it's behavior is what it does when
there is more than one gene in the display.  The dumper appears to
pick one of the genes at random and displays just that one.  I would
guess that it is supposed to display all of them with labels.

Scott


2011/5/13 Aaron Mackey <amackey at pcbi.upenn.edu>:
> Can you help with this Gbrowse question?
> -Aaron
>
> ---------- Forwarded message ----------
> From: 肖金 <xiaojin at genomics.org.cn>
> Date: Thu, May 12, 2011 at 10:04 PM
> Subject: a problem about ProteinDumper in GBrowse2.25
> To: amackey at pcbi.upenn.edu
>
>
> Hi, I have a problem to show protein sequence in GBrowse2.25. When the
> strand of CDS is "+", it can work well. But when the strand is "-", there
> are so many "*" in the sequence, and also it is very difficult to read. I
> think it is a wrong result.
> Thanks! Waiting for your advice.
> --
>
>
> Best wishes!
>
>
>
> 肖 金 Xiao Jin
>
> 深圳华大基因研究院 科学特种兵团
> Bioinformatics Center,Beijing Genomics Institue, Shenzhen
>
> 地址：深圳市盐田区北山工业区11栋2楼
> Address: 2F, Building NO.11, Beishan Industrial Zone, Beishan Road,
> Yantian District,Shenzhen, Guangdong, China
>
> 邮编：518083
> Postal Code: 518083
>
> Phone:13027960219
> Website: www.genomics.org.cn
>
>



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