Genome 540 Homework Assignment 2

Due Sunday Jan. 25

1. Write a program that
   • reads in the FASTA file of coding sequences for the organism (this file has the suffix .ffn, and you should be able to find it in the same place that you found the .fna file having the complete genome sequence);
   • computes a "codon usage table" that counts the total number of times each codon is used (in-frame) in all of the coding sequences (ignoring codons that contain ambiguous nucleotides -- N,R,Y, etc.); and
   • prints out
     • the name of the FASTA file
     • the first line of the FASTA file
     • the number of sequences, and total number of codons, in the FASTA file
     • the codon usage table, in the same format that is used for the genetic code table (e.g. the upper left hand corner gives the number of times that "TTT" is used as a codon).
2. Write a program to find a list of non-overlapping predicted coding sequences in your organism. Specifically, this should
   • identify all ORFs (open reading frames) that start with the codon ATG, GTG, CTG, or TTG, end with a stop codon in the same reading frame (with no intervening in-frame stop codons), and have length at least 100 codons; be sure to do this for both strands of the genome sequence (i.e. the strand given in the .fna file, and its reverse complement); codons that contain ambiguous nucleotides should be counted when determining the length, but should not be eligible to be stop or start codons
   • prune this list of ORFs to eliminate overlapping sequences (removing the shorter one of an overlapping pair), by using the following procedure: first sort the list of ORFs by decreasing size; then work through the list one at a time (starting with the largest ORF), accepting an ORF if it does not overlap any previously accepted ORF, otherwise rejecting it (be sure to reject ORFs that overlap longer ORFs on the opposite strand as well as the same strand);
   • write a FASTA file containing all the accepted ORFs.
3. Run the program you wrote in #1 above on the FASTA file you generated in #2, so as to print out a codon usage table for the open reading frames you found.
4. Email the output from #1 and #3 (but not #2) to me at phg@u.washington.edu AND Chris at ctsa@u.washington.edu. Please make it as compact as possible. Do NOT send the code itself. Include the output in the body of your email message (as plain text), NOT as an attachment.