[Bioperl-l] Should coords be adjusted after removing alignment columns?

Chris Fields cjfields at uiuc.edu
Tue Aug 14 13:19:59 EDT 2007


On Aug 14, 2007, at 12:13 PM, Sendu Bala wrote:
...

>
> Yes. For extra clarity, my thinking is that the correct answer is:
>
> a/6-19            tcgatcatcatc
> b/30-42           tcgatcatcatc
> c/51-63           tcgatcatcatc
>  ...
> What you say in the rest of your discussion is valid and deserves  
> some thought/discussion, but for now just getting the start and end  
> correct, ignoring any issues with internal residues, seems like a  
> no-brainer.
>
> For my own purposes that is all I need; having removed gaps I only  
> need the start and end so I can take that region from each sequence  
> and do a new alignment (for example).

It might be worth addressing the split location issue in the bug  
report before it gets lost in the ether.  Or maybe start a new one as  
an enhancement request.

> BTW. Either my patch isn't quite perfect or there's another related  
> bug I'm still tracking down. I'll commit when I've solved that,  
> unless someone points out any mistakes in my thinking.

Sounds fine by me.

chris



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