needle: Strictly global alignment?

[Peter Rice]

Jan T. Kim wrote:
> Dear EMBOSSers,
> 
> it seems to me that the alignment computed by needle is not a global
> alignment in the strict sense of the term, because the terminal gaps
> are not penalized.
>
> In the literature, a global alignment in which terminal gaps are not
> scored is called a semiglobal alignment.
> 
> If my analysis is correct, I suggest to change the documentation
> accordingly. In addition, it would be nice to extend the needle program
> such that a global alignment sensu stricto can be carried out.

Sorry, but the literature from computer science and maths does not match 
reality for biological sequences.

Remember that you have no information that either sequence is complete.

In bioinformatics, a global alignment is one which spans the full 
extents of the input sequences (e.g. Baxevanis & Ouellette (2001) 
"Bioinformatics" 2nd edition p189. There is no biological reason to 
penalise terminal gaps.

And of course, for many biological purposes, a local alignment is what 
makes sense.

... Though we could add terminal gaps as an option for those rare cases 
where it could be useful. I note that stretcher also does not score 
terminal gaps.

Hope this helps,

Peter