[Bioperl-l] Truncate sequence with features

Roy Chaudhuri roy at colibase.bham.ac.uk
Mon Jun 12 11:46:49 EDT 2006


Hi Heikki.

> Two questions come to mind:
> 
> 1. Can you parse your joint location using bioperl without errors?
Seems to work fine as far as I can tell (no errors, and to_FTstring 
reproduces the location as expected).

> 2. Is there a practical advantage in including a location which has no 
> relevance to the sequence in hand?
I think it would be misleading to imply that a location was complete 
when it is only a part of the originally annotated feature. From the FT 
definition the other possibility would be to include the missing parts 
of the feature as remote locations, I guess that may be more satisfactory.

Roy.
--
Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.

http://xbase.bham.ac.uk


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