[Bioperl-l] contig disassembly

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Wed Jan 17 09:29:17 EST 2007


Hi, Andrew, 

I am not sure you are aware 0f NCBI Map Viewer:
 
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&gnl=NT_079540.1&
maps=comp,genes&cmd=txt

Here is an example to retrieve components and genes from NT_079540.1 of
current Hs. genome build 36.2.

Wenwu Cui, PhD
National Center for Biotechnology Information
National Institutes of Health
Bethesda, MD 20892


-----Original Message-----
From: Andrew Stewart [mailto:stewarta at nmrc.navy.mil] 
Sent: Tuesday, January 16, 2007 4:12 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] contig disassembly

If I want to take a Bio::Seq object representing a contig and  
disassemble it into the constituent sequences which originally lead  
to its formation, all the while preserving the feature annotation  
associated with each sub-sequence, and with the coordinates of these  
feature sets updated to reflect their position relative to these sub- 
sequences, what is the best way to go about this?  If I take a  
subsequence of a Seq object, will it carry over the relevant features  
as well?


--
Andrew Stewart
Research Assistant, Genomics Team
Navy Medical Research Center (NMRC)
Biological Defense Research Directorate (BDRD)
BDRD Annex
12300 Washington Avenue, 2nd Floor
Rockville, MD 20852

email: stewarta at nmrc.navy.mil
phone: 301-231-6700 Ext 270


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