----- Original Message ----- From: "WC -Sx- Jones" <[EMAIL PROTECTED]> To: "Öznur Tastan" <[EMAIL PROTECTED]> Cc: "'Perl Lists'" <[EMAIL PROTECTED]> Sent: Tuesday, February 24, 2004 9:33 PM Subject: Re: how to push a double dimensional array
> Öznur Tastan wrote: > > >>>so my alignments has three features(seq1 seq2 and the score of the > >>>alignments) > >>>seq1: AADALLL > >>>seq2: - - EVLLL > >>>score:12 > > > OK, so alignment > > L > E > > is 17 but because > > A D > - - > The result is (12+5)-(1+4) or 12? I didn't exactly understand this line but if you are alignment of L E can be 17 (though not very likely because they are not that similiar aminoacids:) but AD - - will be definitely negative since the both A and D is aligned with gaps that will be penalized. if a linear gap penalty scheme is used and say the gap penalty is -5 the score of the alignment will be -10 > -Sx- > > -- > To unsubscribe, e-mail: [EMAIL PROTECTED] > For additional commands, e-mail: [EMAIL PROTECTED] > <http://learn.perl.org/> <http://learn.perl.org/first-response> > -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] <http://learn.perl.org/> <http://learn.perl.org/first-response>
