Working in Unix

The Unix compendium "An Introduction to Unix" is useful in this assignment.

In these assignments, you will need to use Unix redirection of input and output.

1. Take a look at the large file /info/DD2404/appbio16/data/gpcr.tab using head. This file contains data concerning G-protein coupled receptors from a number of species.head. How many columns are there (if you count by eye)?

   If you work on your own computer: download this file to work on.

2. How many lines is there in the file?
3. Use grep and wc to find out how many human GPCRs there are listed. Do you search for "human" or "Homo sapiens"?
4. How long is the shortest sequence listed in the same file? Use cut and sort!
5. How many species are named in gpcr.tab?
6. Use a for-loop to apply multi-sequence alignment program muscle to the data files in /info/appbio15/data/testatin/*.fa. If you work on your own computer: download this file (gzipped tar file) to work on.
   1. Figure out what muscle does and how you run it. (Sorry, no man-pages.)
   2. You have to use a for-loop in bash. Repeated manual invocation is not allowed in this course.
   3. Each run should have its own output file.

To present:

1. You should be able to show and explain what you have done to the teacher.
2. You are expected to understand how the commands work.