Perl for Bioinformatics

This semester, I learn a lot of perl and linux system, the followings are useful links, I found them when I did my homework:
Bioperl tutorial
FTP download blast database
Perl: Subroutines
Regular Expression
Tutorial for awk

1. Linux system: I started to use Ubuntu system since this summer, when I took "Introduction to database". At first, I tried to install mysql and Java on windows, but I failed. When I went to ask our TA, they told me:"Sorry, we don't know how to install it on window, we only know Ubuntu". That's the first time I heard of Ubuntu, and then I installed it. That's the rule, if all the people use one system or programming language, I'd better use the same one, since it's easy to be compatible when you are working. Actually, Ubuntu has a lot of advantage. It's fast, and the software center is awesome, you don't need to worry about download and upgrade/update, it will automatically do it.

2. Perl: I learned perl last year in Bioinformatics class, but not systematically and professionally. This semester, I learned it more deep, including objected oriented programming, and multiple thread. Bioperl is really huge, and contains a lot of module, it even has some software as a module, like GENEWISE and GENESCAN, and we can parse the output as an object. However, my experience tell me you'd better use "system" to run it and parse the output file using regular expression by yourself, since you may know what is happening when the program trows exceptional!! I only used GENEBANK and BLAST object on Bioperl, since I think these two are well developed. Other software, I'd rather parse the file by myself.

3. Bioinformatics: Also, from this course, I have a systematical conception of bioinformatics and its problems which need to be solved.
Shotgun sequences--->(Assemble)--->Contigs---->(gene prediction)---->genes---->(phylogenetic analysis)---->phylogenetic tree---->biological meaning
In next semester, computational genome, I will learn more about these problems.