Hashes (hw4)
Remember hashes? They are like arrays, a collection of boxes. The main difference is that each box has a name instead of a number. Today’s homework is about hashes!
Continue reading
Perl & Genomics
Bioinformatics for Genomics Course – University of Padua
Category Archives: homeworks
Homework: reviewing Perl basics
Review homework (hw3)
If you have Linux on your laptop you can download the program and change it with a text editor like we did in the lab. Note that your Linux may be a little different, so you may need to looks for the Terminal and the Text Editor, but they are there somewhere. If you do not have Linux yet, you can use codepad. This task is coded “hw3” (not hw-3 or hw-03…. right?).
Homeworks: Arrays and foreach
Arrays and the foreach loop hw2
In this homework we are going to do some simple changes to a perl program, like we did during the last lab session. If you have Linux on your laptop you can download the program and change it with a text editor like we did in the lab. Note that your Linux may be a little different, so you may need to looks for the Terminal and the Text Editor, but they are there somewhere. If you do not have Linux yet, you can use codepad. This task is coded “hw2“. Continue reading
Homeworks: testing conditions
IF homework (hw1)
This is the first official homework you get! In this homework we are going to do some simple changes to a perl program, like we did during the last lab session.
If you have Linux on your laptop you can download the program and change it with a text editor like we did in the lab. Note that your Linux may be a little different, so you may need to looks for the Terminal and the Text Editor, but they are there somewhere. If you do not have Linux yet, you can use codepad. This task is coded “hw1“.
Homeworks
Dear guys,
we are really happy as we can see your efforts and your improvements. On Friday we’ll meet in Aula M Pr at 11.30, for a comprehensive course on Perl, so remember to repeat this part at home, try changing things in the scripts…
It’s going to be a long journey!
Calculate your oligonucleotide resuspension volume
As promised during today’s lecture, here you have your homework:
please calculate the amount of water to be added to each of the primers in the list, in order to produce a working solution of 10 µM. You can produce a concentrated stock solution and then dilute the stock solution to a working solution of 10 µM, if it is needed.
Oligonucleotide datasheet containing all the information as provided by the supplier
Did you managed to find the right volume for each stock solution?
The Hamilton pipetter needs you to provide a coordinate and a volume separated by a tab for each of the primer. The information concerning each of the primers must be separated by a new line character, as shown in the example below
example of coordinate's file that you should pass to the Robot, to guide it (him?) doing the pipetting for you
Now try to translate the work that you performed to get this result into a list of actions (the algoritm).
For the most willing students, this is the moment for translating your algoritm into a Perl program and testing it at volume calculation for this short primer’s list.
Very soon you will find the solution on this blog. Stay tuned
An (optional) exercise to test your skills
Look at our pick-primers.pl script: I added some ASCII characters to draw a box around the welcome screen. Now it looks like:
print STDERR " +----------------------------------------------+ | Pick Primer Tool v.01 | | | | Parameters: | | contig1 direction1 contig2 direction2 | | | | direction1,2 = U or C | +----------------------------------------------+ "; |
A small game: guess what this script does
Below you’ll find a script.
Guess what’s the purpouse of the program… and if you like it give him a try.
Write me your guess at 
. I’ll post both the solution and a test on the ouput produced on Mar 25th.
Parse BLAST output (tabular format)
We performed a BLAST aligment using the -m 8 parameters, that produces a tabular format.
Let’s review how to parse it with Perl.
Solutions to some Perl scripts
Here I post some scripts, with comments: minimum and maximum, reverse complement a sequence and reverse and complement a sequence stored into a file.