----- Original Message ----- From: "WC -Sx- Jones" <[EMAIL PROTECTED]> To: "Öznur Tastan" <[EMAIL PROTECTED]> Cc: "'Perl Lists'" <[EMAIL PROTECTED]> Sent: Tuesday, February 24, 2004 9:53 PM Subject: Re: how to push a double dimensional array
> Öznur Tastan wrote: > > >>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 > > A-Z = 1-26 > > L = 13 + E = 5 > ______________ > 17 > So you see where my confusion is coming from. :))) no actually the pairs has a score according to how similiar(in biological sense) A(Alanine) and V(Valine) will have a positive score when they have paired up since their biochemical nature resembles. > -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>
