----- Original Message ----- From: "WC -Sx- Jones" <[EMAIL PROTECTED]> To: "Öznur Tastan" <[EMAIL PROTECTED]> Cc: "R. Joseph Newton" <[EMAIL PROTECTED]>; "Charles K. Clarkson" <[EMAIL PROTECTED]>; "'Perl Lists'" <[EMAIL PROTECTED]> Sent: Tuesday, February 24, 2004 9:05 PM Subject: Re: how to push a double dimensional array
> Öznur Tastan wrote: > > Ok: I am starting from the beginning. > > > > The alignment is alignment of two strings so that similiar characters > > according to a scoring system(this is out of scope I think) should be in the > > same register and there can be gaps in one of the strings denotes as a dash. > > so my alignments has three features(seq1 seq2 and the score of the > > alignments) > > seq1: AADALLL > > seq2: - - EVLLL > > score:12 > > > I guess I am thick as a brick because I am more confused now then when > this thread started. > > How does alignment equate to score? > Only using the example given? Well actually storing the examples doesn't need the information for the alignment but if you are interested. Pairwise sequence alignment is a widely used terms to visualize the similarity of protein or DNA sequences. So the characters denotes the aminoacids(or nucleotides in DNAs) and the conservation substitutions or deletions of give clues about biological meanings actualy predict the evolution at that site of the protein. Substitution scoring matrices which are mostly based on frequency analysis are used to align the alignments. These are matrices that tell how similiar one aminoacid to another so to say how it is likely to be replaced by the other aminoacid. so Aligning L with L will have positive score that you can get from the scoring matrice entry yet the gaps will be penalized although mismatches will be penalized. The alignment is obtained by using a dynamic programing appraach, Needleman-Wunch algorithm. The score is the sum of the score of aligning each character. > > I await the conclusion and enlightment as this thread has proven > interesting. :) > > Thx/Sx -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] <http://learn.perl.org/> <http://learn.perl.org/first-response>
