Problem Sets

Be sure to check out for the tests!


Alter the greeting script to accept the flag "--excited" that adds an exclamation point to the end of the greeting:

$ ./greet.pl6 --excited --greeting="Hola" --name="Amigo"
Hola, Amigo!

Sum and mean

Create a script that reads in numbers from the command line and prints out their sum and mean.

Clean sequences

Write a bash script to clean up some raw sequence.

Create a FASTA file

Create a script called "txt2fasta.pl6" that accepts an input file of sequences, one-per-line, and emits FASTA-formatted sequences. Sequence IDs should be an incrementing integer value starting at 1. Extra credit: block the sequences to a maximum column width, default 50.

FASTA stats

Given one or more input files of sequences in FASTA format, recreate this output:

$ seqmagick info mouse.fa | awk '{print $1,$3,$4,$5,$6}' | column -t
name      min_len  max_len  avg_len  num_seqs
mouse.fa  50       100      84.32    500

Compute GC content

Solve the GC content problem on Rosalind ( Then use that program to profile FASTA files and predict species.

Find motifs

Solve to find motifs in strings. Use this to find ORFs.

Compute Hamming

Solve to find the number of mutations (SNPs/SNVs) between two sequences. Use this to determine sequence similarity.

Protein translation

Solve Read the translation table from the given "table.txt."

Shared k-mers

Create a program that will find the number of shared k-mers of a given size among a set of sequences in a FASTA file. Use this to determine sequence similarity. You can use the "fasta-kmer" program to create a list of k-mers in the given sequences.

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