Fall11 > TWikiUsers > TahouraSamad > TahouraSamadHomework3

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My program for this assigment is attached as simulator.pl.txt, and the FASTA files I tested it on are attached as testsequence1.txt and testsequence2.txt. Given composition parameters, it can load parameters and generate random sequences for 1 or more sequences in a FASTA file. Given a FASTA file with 1 or more sequences, it can generate random FASTA files with the same composition of the original sequences in the FASTA file. I've also included samplefile.txt, a sample txt file that I load parameters from and that my program saves parameters to. The file contains the name, the total length, number of each nucleotide in the sequence as well as the percentage of each nucleotide in the sequence for each sequence in a fasta file. All lines are preceded by a > except for the name, which is preceded by >> and the length and number of each basepair, which are preceded by nothing. This makes it easy for the program to find the number of each nucleotide and total length and generate a random FASTA file from them. The percentages are included because I thought that was a more useful representation of the composition than the indiviudal numbers of each nucleotide.

I	Attachment	Action	Size	Date	Who	Comment
txt	samplefile.txt	manage	0.3 K	2011-10-09 - 01:53	TahouraSamad
txt	simulator.pl.txt	manage	8.6 K	2011-10-09 - 01:52	TahouraSamad
txt	testsequence1.txt	manage	7.7 K	2011-10-08 - 23:29	TahouraSamad
txt	testsequence2.txt	manage	1.3 K	2011-10-09 - 01:52	TahouraSamad

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