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Here is a part of the code that I have pasted followed by my question. This program uses, perl and one function below uses bioperl to obtain all the possible sequences from a given degenerate iupac string

For example, I will use the iupac string here as:

'NNYDBAVDVHVHNGGNR'

Here, A,C,G, or T are single characters, everything else either carries 2, 3 or 4 characters as follows:

N => ACGT

Y => CT

D => AGT

B => CGT

V => ACG

H => ACT

R => AG

So we can see how many possible combinations can come out of this iupac string probably >10000000 seqs with only A,C,G or T characters

#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::SeqFeature::Primer; use Bio::Tools::IUPAC; use Bio::Tools::SeqPattern; #some parameters for the equation to compute Tm my $conc_primer = 0.25; my $conc_salt = 50; my $mgconc = 0; my $iupac = 'NNYDBAVDVHVHNGGNR'; #this calls the function to generate all possible seqs from iupac stri +ng my @PotSeqs = find_degenerates($iupac); my @Tm_Thermodynamic=(); foreach my $PotSeqs(@PotSeqs){ #this call the function to compute tm for each seq my $Tm_Thermodynamic = tm_Base_Stacking($PotSeqs,$conc_primer,$conc_sa +lt,$mgconc); push(@Tm_Thermodynamic, $Tm_Thermodynamic); #I have to add a function here to get the min and max tm values +from the Tm_thermodynamic array filled above # printf "%.4f", $Tm_Thermodynamic_min; # print "\t"; # printf "%.4f", $Tm_Thermodynamic_max; # print "\n"; } #function to get all possible combination of an iupac string sub find_degenerates { my $sequence = $_[0]; my $seq_obj = Bio::Seq->new(-seq => $sequence, -alphabet => 'dna') +; my $stream = Bio::Tools::IUPAC->new(-seq => $seq_obj); my @oligomers; while (my $uniqueseq = $stream->next_seq()) { push @oligomers, $uniqueseq->seq; } return @oligomers; } #Function to compute the Temperature for a given sequence (sequence va +lid only if contains A,C,G or T) sub tm_Base_Stacking { my ($c,$conc_primer,$conc_salt,$conc_mg) = @_; my $c_len = length($c); my $h=0; my $s=0; # enthalpy values my %array_h = ( 'AA'=> '-7.9', 'AC'=> '-8.4', 'AG'=> '-7.8', 'AT'=> '-7.2', 'CA'=> '-8.5', 'CC'=> '-8.0', 'CG'=> '-10.6', 'CT'=> '-7.8', 'GA'=> '-8.2', 'GC'=> '-10.6', 'GG'=> '-8.0', 'GT'=> '-8.4', 'TA'=> '-7.2', 'TC'=> '-8.2', 'TG'=> '-8.5', 'TT'=> '-7.9' ); # entropy values my %array_s = ( 'AA'=> '-22.2', 'AC'=> '-22.4', 'AG'=> '-21.0', 'AT'=> '-20.4', 'CA'=> '-22.7', 'CC'=> '-19.9', 'CG'=> '-27.2', 'CT'=> '-21.0', 'GA'=> '-22.2', 'GC'=> '-27.2', 'GG'=> '-19.9', 'GT'=> '-22.4', 'TA'=> '-21.3', 'TC'=> '-22.2', 'TG'=> '-22.7', 'TT'=> '-22.2' ); #correction for salt concentration my $salt_effect= ($conc_salt/1000)+(($conc_mg/1000) * 140); # effect on entropy $s+=0.368 * ($c_len-1)* log($salt_effect); # compute new H and s based on sequence. for(my $i=0; $i<$c_len-1; $i++){ my $subc=substr($c,$i,2); $h+=$array_h{$subc}; $s+=$array_s{$subc}; } my $rlnk = ($conc_primer/2000000000); my $r = log10($rlnk); #equation to compute the Tm my $tm=((1000*$h)/($s+(1.987*$r)))-273.15; return $tm; } #function to take the log sub log10 { my $n = $_[0]; return log($n)/log(10); }

my question is how can I make this efficient. I only am looking for the range that is Min and Max Tm or temperature values for a given iupac string. Here, what I am doing is I am computing Tm for every possible seqs of a given iupac to get the accurate range, but this is too slow and inefficient.. I am running totally out of memory and it becomes worse when iupac degeneracy increases. Is there a way I can make it efficient and still be able to get more or less an accurate range (min and max Tm values)?

I would appreciate any help/suggestions. Please let me know if I need to further explain anything.


In reply to how to make this code more efficient? Need to Compute the Min and Max of a Temperature using an equation by BhariD

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