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Hi rharsh, Thank you so much! Is "print "Pairs: ",@pairs,"\n";" to print the negative pairs? Thanks again!

the updated code as below: my @fullset = qw(AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT); my (@major, @minor, @combinations); { my @temp = @fullset; foreach (0..3) { my $r_pair = splice(@temp, int(rand($#temp+1)), 1); $major[$_] = $r_pair; } } foreach my $pos (0..$#major) {...

...nucleotide pairs and need your help. I have enclosed the description of the question and my code here. Any suggestion is highly appreciated. *********************************** The description To generate negative dependent pair binding sites for motif 1. We can get 16 combinations of...

It works! Thank fish!

hi fish, I doubt line 51 is within open OUTPUT, "> outfile9_55_$y.txt" or die "Cannot open output file.\n"; foreach (@combinations) { print OUTPUT join('', @{$_}), "\n"; } thanks

Hi rharsh! I tried that code. Although the message "Use of uninitialized value in join or string at make_file2.pl line 51" still exsited, it seemed that that code can generate the right results. Thank you again!

Thank rharsh for help! That code does work! But what is the problem in my first code? Thanks again! Alex

...of major pair, num records to generate # This is a basic ceiling function for $num_major for ($y=0; $y<=99; $y++) { my $num_major = ($prob / 100) * $records; if ($num_major != int($num_major)) { $num_major = int($num_major++); } my $num_minor = $records - $num_major; { my @temp = @fullset...

...of major pair, #num records to generate # This is a basic ceiling function for $num_major for ($y=0; $y<=99; $y++) { my $num_major = ($prob / 100) * $records; if ($num_major != int($num_major)) { $num_major = int($num_major++); } my $num_minor = $records - $num_major; { my @temp = @fullset...

Dear all, Thank you for warm help! I prefer "open (SHORT, "< outfile8.txt"); chomp (@short = <SHORT>); close SHORT;" for the input. BTW, can the code be slightly modified to print the result like: 37 26 26 56 32 22 36 47 (Note: each number is the highest frequency of the nucleotide in...

I see! Thank you! But can you remove the output like "0 | G 1 | A 2 | C 3 | T 4 | T 5 | G 6 | A 7 | A" ?

Hi Duncan, I put the data in the code and got the result like: 0 | C 1 | G 2 | A 3 | T 4 | T 5 | A 6 | G 7 | C 0 | T 1 | A 2 | C 3 | T 4 | T 5 | A 6 | G 7 | A 0 | A 1 | C 2 | C 3 | C 4 | A 5 | C 6 | C 7 | G 0 | C 1 | T 2 | G 3 | A 4 | G 5 | T 6 | T 7 | C 0 | T 1 | G 2 | T 3 | C 4 | A 5 | T...

should I include the data in the code?

Hi Duncan, I ran the 1st script. The output is: A: conclusion C: conclusion T: conclusion G: conclusion What is the problem? Thanks, Alex

Hi! I have a txt file which holds 100 sequences and the width for each sequence is 8 nucleotide long. Like: AGATAGCA ACACAGTA TCCGTGCT ATTGGCTA GACTTGAA ........ I want to calculate the frequency of nucleotides A,T,C,G for each column NOT each row and print them out. My code is here but it...

Hi rharsh, Thanks for the message! I changed the code as you suggested and run into the result like: CCAGCGCT CCAGCGCT AAATCGCT CCAGCGCT CCAGACCT AAAGCGCT CCAGACCT CCAGCGTG CCAGCGCT CCAGCGCT CCATCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCATCGCT CCAGCGCT CCAGACCT CCAGACCT...

Hi Kevin, Thanks! Since we had to change our ideas, the code should be changed slightly. BTW, I fixed another code which used subroutine. Thanks again!

...we thought that we would have to switch to another idea because the previous data was not what we really want. My previous description was: ************************************************** I am going to generating 100 8 base-pair long dependent motif binding sites using Perl. The thread...

Thanks! In case that I need the number other than 100, I guess I can change the probability accordingly. Right? Thanks!!!

so what is your suggestion? you mean it will generate more than 100 sequences?