[Bioperl-l] What's the best object to store sequence assembly information?

[David Yerushalmi]

Hi,

I am working on an object that stores information from
a Celera SNP XML file.  Each record contains data
about a specific dna sequence that was used in an
assembly during snp discovery.  Here's the information
i need to encapsulate:

1)  bioseq_id

2)  assembly_begin

3)  assembly_end

4)  orientation

5)  offset

The XML record looks like this:

{POLY_INSTANCE_ASSEMBLY}

              {BIOSEQ_ID}12345{/BIOSEQ_ID}

              {ASSEMBLY_BEGIN}617{/ASSEMBLY_BEGIN}

              {ASSEMBLY_END}617{/ASSEMBLY_END}

              {BIOSEQ_TYPE}2{/BIOSEQ_TYPE}

              {ORIENTATION}+{/ORIENTATION}

              {OFFSET}0{/OFFSET}

       {/POLY_INSTANCE_ASSEMBLY}

Do you have any suggestions on what existing bioperl
class if any would be suitable to store this
information? 

-david



__________________________________________________
Do You Yahoo!?
HotJobs - Search Thousands of New Jobs
http://www.hotjobs.com