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Hi,all! I am going to generate some nagative dependent 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...

Hi all, I got an error message when running the code at the end of this post. It said that "Use of uninitialized value in join or string at make_file2.pl line 51." Although I doubt the error message, I would appreciate if you can find something I really missed. Thank you! 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 all, Thank you so much for help on this topic. After discussing with my advisor, 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...

Hi all! I have two separate codes and want to integrate them into one. (1)1st code is to use a short sequence of width as 8 or 16 as a template to generate 100 short sequences of the same width and store them in a txt file A. (2)2nd code is to read 100 short sequences from the txt file A...

Hi! My code is to generate 100 sequences (width=8) and print them on the screen. Now I want to write these sequences to a file and make sure each sequence per a line. My code is : ***************************** #!/usr/bin/perl # randommotifs.pl use strict; use warnings; my $N_Sequences = 100...

Hi all, I want to generate a random motif of width 8. Each position will have a dominant letter with probability around 0.85. Repeat this to generate 100 motifs. For example, I have a motif like: ATCGTGCC The first nucleotide is A and its probability is 0.85, which means the probability of...

Hi all! I asked a question about "how to handle two files simultaneously" several days ago and a couple of people gave me very useful tips. Thanks again! Bascially, "short_sequence.txt" file holds 100 short sequences (8 nucleotide long)and "long_sequence.txt" file holds 100 long sequences...

Hi all! I use code (see below) to generate a bunch of sequences like: ************************************************ 46 8...

Hi all![noevil] I am going to generating multiple 8 base-pair long dependent motif binding sites using Perl. The thread is: (1)First,randomly select 4 pairs of nucleotides as the group A. For example, we randomly select 4 pairs of nucleotides, “CA”, “TG”, “CG”, and “TC” from 16...

Hi all, I have two txt files to handle. One is "short_sequences" and the other one is "long_sequences". The "short_sequences" holds 100 short sequences (8 nucleotide long) and 100 long sequences (200 nucleotide long) in the "long_sequence". For example, the first short sequence is "TTGACATA"...