[Biococoa-dev] starting BCAlignment

[Philipp Seibel]

The piece of code alex just sent arround is great to understand what a 
global alignment is. Alex uses two types of scores, a match and a 
mismatch score, this is the simplest way to align sequences. It 
produces quite good alignments for dna sequences, but in the most 
common cases, you need the scoring matrix to score different kind of 
matches and mismatches. Another point is to differentiate between 
gap-open and gap-extension costs, but this is more relevant at local 
alignments.
Ok i stop here, because nobody can follow me anymore ..... ;-)

Phil