[Bioperl-l] LocatableSeq NSE format - suggested changes
cjfields at illinois.edu
Mon Dec 14 20:23:05 EST 2009
The current output for NSE format (Name/Start-End) via Bio::LocatableSeq::get_nse() currently doesn't allow for strandedness. I have seen two variations of NSE that incorporate strandedness:
1) Stockholm Rfam reverses start and end if the strand == -1
2) Sheldon McKay's Gbrowse_syn uses Name(strand)/start-end
The former breaks fewer things within BioPerl, but the latter seems more explicit. Any preferences? Do we want a new method that creates this, and deprecate out simple non-stranded NSE?
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