----- Original Message ----- From: "Charles K. Clarkson" <[EMAIL PROTECTED]> To: "'Öznur Tastan'" <[EMAIL PROTECTED]>; "'Perl Lists'" <[EMAIL PROTECTED]> Sent: Tuesday, February 24, 2004 8:59 PM Subject: RE: how to push a double dimensional array
> Öznur Tastan <[EMAIL PROTECTED]> wrote: > : > : > : Ok: I am starting from the beginning. > > I thought I had accidentally discouraged you. > > > : The alignment is alignment of two strings so that similar > : 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. > > What do you mean by "should be in the same register"? What > is a register? Like in the alignment below A is in the same 'register'( bad English himm:) with - but seq1 and seq2 have these information already so when I know seq1 and seq2 I don't need any further information to visualize the alignment. three feature is enough to define my alignment AADALLL - - EVLLL the alignment is there ( this is pairwise alignment of protein sequences that can be calculated by dynamic programming of two strings) > : So my alignments have three features (seq1 seq2 and the score > : of the alignments) > : seq1: AADALLL > : seq2: - - EVLLL > : score:12 > : > : There are groups of alignments that I want to keep separated. > : Say I have 15 alignments (the numbers and distributions can > : be changed with different input strings) > : 3 of the alignments belong to first group > : 4 of them second belong to 2nd group. > : 5 of them belong to 3rd > : 2 of them belong to 4th > : 1 of them belong to 5th) > > What is a group of alignments grouped by? Is it by score > or some other quality? no not score some other quality related to origins of the sequences ( again related to biology ). so the alignments of certain sequence pairs should belong to one group and the others another.so we for the scope of problem believe me it is not important. > : Since later on I am going to build longer alignments by taking > : one alignment from each group in order and concatenating them > : (all combinations), I need to store the alignments group by > : group. Note I know the group numbers in advance. > > What are "group numbers"? I meant the say number of groups. > : So what approach and what data structures would you > : recommend me to use? > > It's too soon to tell. You'll need to answer the questions > above to get a better answer. hope I was clear. oznur > > > > > > -- > 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>
