[Bioperl-l] parsing coded_by subfeature

[Jack Chen]

Thanks Jason! I have looked into the script before but it does not
actually handle the join cases though. 

I am also curious how to handle the cases where the 'coded_by' subfeature
contains the ">" and "<" signs. I am not really sure what they mean. And I
noticed that wherever these signs appear, the protein sequences retrieved
are different from the conceptual translation from the nucleotide
sequences. For example:

[nchen at whey blast_db_checked]$ ./test.pl "gi|8573628|gb|AAF77462.1|"
Protein obtained from GenBank:
MPQMAPISWLLLFIIFSITFILFCSINYYSYMPNSPKSNELKNINLNSMNWKW
CDS sequence is:
ATCCCACAAATAGCACCAATTAGATGATTATTACTATTTATTATTTTTTCTATTACATTTATTTTATTTTGTTCTATTAATTATTATTCTTATATGCCAAATTCACCTAAATCTAATGAATTAAAAAACATCAATTTAAATTCAATAAACTGAAAATGATAA
Conceptual translation is:
IPQIAPIR*LLLFIIFSITFILFCSINYYSYMPNSPKSNELKNINLNSIN*K**

Jack 

++++++++++++++++++++++++++++++++++++++++++++
    o-o     Jack Chen, Stein Laboratory      
    o---o   Cold Spring Harbor Laboratory    
  o----o    #5 Williams, 1 Bungtown Road           
 O----O     Cold Spring Harbor, NY, 11724   
 0--o       Tel: 1 516 367 8394              
   O        e-mail: chenn at cshl.org  	    
  o-o       Website: http://www.wormbase.org
+++++++++++++++++++++++++++++++++++++++++++++
        


On Sun, 20 Jul 2003, Jason Stajich wrote:

> See the FAQ this question #5.4
> http://www.bioperl.org/Core/Latest/FAQ.html#Q5.4
> 
> -jason
> On Sat, 19 Jul 2003, Jack Chen wrote:
> 
> > Hi All,
> >
> > I'd like to retrieve nucleotide sequence for a give protein sequence. I
> > know that I could do it through coded_by subfeature, which can be rather
> > messy. Say, it could be one of the following formats
> >
> > 	 #AF264924.1:1749..>2110
> >          #AF264924.1:<254..1563
> >          #join(AY260053.1:497..545,AY260053.1:610..3342,
> > AY260053.1:3409..3750,AY260053.1:3810..4511, AY260053.1:4569..4960)
> >
> > Is their a good and unified way to do it?
> >
> > Thanks
> >
> > Jack
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>