I think he asked something like this.. But I am not clear with his question..
#!/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);
$prob{$triplet}++;
$k+=3;
}
while ( ($triplet,$val) = each %prob ) {
print "\n $triplet occured $val times \n";
}
-----Original Message-----
From: km [mailto:[EMAIL PROTECTED]
Sent: Friday, March 05, 2004 4:10 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
>
--
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>
