......or code/algorithm will be appreciated.
Overview: Obtain a dna FASTA sequence and randomly shuffle the sequence while maintaining the overall distribution of bases. Randomly shuffle the sequence 10-20 times, i.e.
randomly select a number greater than 10 but less than 20 and then proceed to shuffle the sequence that many number of times. Then measure the similarity between the shuffled sequence versus the original sequence by scoring. (z-scores).
Scoring criteria:
If a purine was mutated to a purine, or a pyrimidine to a pyrimidine assign a value of +1 to that base pair. If a purine was mutated to a pyrimidine or vice versa assign a value of -1 to that base pair. If the base pair did not change assign 0 .e.g.
Original: A C G T A G C T
Mutated: A T T A C G A T
Score = 0+1-1-1-1+0-1+0 = -3
A and G are purines
C and T (U in RNA) are pyrimidines
Okay, so i think i understand the problem in general but just dont know how to even go about it. Please help explain......if u cant help, thats okay. Just dont insult me for posting this. Please.
thank you.
Overview: Obtain a dna FASTA sequence and randomly shuffle the sequence while maintaining the overall distribution of bases. Randomly shuffle the sequence 10-20 times, i.e.
randomly select a number greater than 10 but less than 20 and then proceed to shuffle the sequence that many number of times. Then measure the similarity between the shuffled sequence versus the original sequence by scoring. (z-scores).
Scoring criteria:
If a purine was mutated to a purine, or a pyrimidine to a pyrimidine assign a value of +1 to that base pair. If a purine was mutated to a pyrimidine or vice versa assign a value of -1 to that base pair. If the base pair did not change assign 0 .e.g.
Original: A C G T A G C T
Mutated: A T T A C G A T
Score = 0+1-1-1-1+0-1+0 = -3
A and G are purines
C and T (U in RNA) are pyrimidines
Okay, so i think i understand the problem in general but just dont know how to even go about it. Please help explain......if u cant help, thats okay. Just dont insult me for posting this. Please.
thank you.