[Bioperl-l] contig disassembly

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Wed Jan 17 14:29:17 UTC 2007

Hi, Andrew, 

I am not sure you are aware 0f NCBI Map Viewer:

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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