Hi, Well thats fine . KM ---------------------------------------------------------- On Fri, Mar 05, 2004 at 01:29:36PM -0800, Sumit Kaur wrote: > Hey , > > I am not considering all the frames . Just the first combination. I am using the > book Learning perl for my basics. > > Thanks and Best Regards, > > Sumit > > -----Original Message----- > From: km [mailto:[EMAIL PROTECTED] > Sent: Friday, March 05, 2004 1:10 PM > To: Sumit Kaur > Cc: [EMAIL PROTECTED] > Subject: Re: Nucleotide Sequence > > > Hi, > > can u pls be a bit clear abt the question. > are u considering all 6 frames while generating combinations ? > u'll have to be comfortable with basics of Perl. > > As far as i have understood ur question i have made a program. > HTH, > regards, > KM > > ########## program ##### > #!/usr/bin/perl -w # change it to ur perl path > use strict; > my $seq = "ATGCCGCTGGTG"; # sequence > my $hops = int(len($seq)/3); > my %prob = ("ATT"=>0.1); # triplets to probabilities mapped > my $sum = 0; > > while($k <= $hops) > { > my $triplet = substr($seq,$k,3); > $sum += $prob{$triplet}; > $k+=3; > } > print $sum; # total > ########## program ############## > > ------------------------------------------------------------- > In-Reply-To: <[EMAIL PROTECTED]> > > On Fri, Mar 05, 2004 at 12:11:25PM -0800, Sumit Kaur wrote: > > Hi, > > > > I have to write my first Perl script . This scripts Searches for rare codons in > > nucleotide sequence . The nucleotide sequence is entered by the user in the format > > "ATTGCAATT.." and then the scripts breaks this sequence in the groups of three > > alphabets like ATT,GCA,ATT...so no.and then I have a list of the combinations and > > their probabilites like ATT (34.4) . I compare the breaked sequence against this > > list and print out the total that is the sum of all the similar combis > > Please suggest . > > > > Thanks > > > > > > >
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