needle: Strictly global alignment?

[Jan T. Kim]

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. As an example, the alignment of sequences seq1 to
seq2 has the same score as the alignment seq1long to seq2 in the
attached file.

Some code delving (EMBOSS-2.6.0/nucleus/embaln.c, function
embAlignPathCalc) indicates to me that no gap penalty is taken
into account when the top row and the left column of the matrix are
initialized, meaning that terminal gaps at the left border of the
alignment will not be scored.

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.

Kind regards,
Jan T. Kim
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: kim at inb.uni-luebeck.de                          |
 |    *NEW*    WWW:   http://www.inb.uni-luebeck.de/staff/kim.html    |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*
-------------- next part --------------
> seq1
ctgcctgt
> seq1long
actgcactaactgcctgtaactga
> seq2
ctgcggctgt