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.

* Take a look at the large file /info/DD2404/appbio156/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.

* How many lines is there in the file?
* Use grep and wc to find out how many human GPCRs there are listed. Do you search for "human" or "Homo sapiens"?
* How long is the shortest sequence listed in the same file? Use cut and sort!
* How many species are named in gpcr.tab?
* 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.
* Figure out what muscle does and how you run it. (Sorry, no man-pages.)
* You have to use a for-loop in bash. Repeated manual invocation is not allowed in this course.
* Each run should have its own output file.

To present:

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