HTML is the very simple language to format web pages. We used HTML as a first use of “simple text” files and our text editor.
Here i report a simple example very similar to the one covered during the first lesson.
<html> <body> <h1>Hello World!</h1> <p>My first paragraph. Another <strong>great</strong> paragraph!</p> </body> </html> |
If you want to test some HTML code without having to create a new text file you can try this website.
During our first lesson we had a brief overview of the sequencing strategy used for Nannochloropsis.
First, a whole genome shotgun approach was used to have a first draft (see picture below). In particular we used the Roche 454 machine that provides reads ~500bp long, and we assembled them with the Newbler package.
As we saw both read length and sequence coverage affects the quality of the assembly. In particular repeated regions make the assembly program to “break” the sequence. This happens if the length of the repeated region is longer than the single fragments (reads) sequenced. Repeated regions collapse in the same contig, that will have a higher coverage (approximately n-times the average, where n is the number of repeats in the genome).
We discussed the project goal: a program to design primers for genome finishing.
We introduced the three main tools of the bioinformaticisists: scripting languages, relational databases and HTML for web interfaces.
You were suggested to download and install a programming editor, with syntax highlighting and other advanced features usually lacking on simpler editors and to install Perl if you use Windows.
If you have Linux or Mac OS X you have Perl installed by default. For Windows users there are different package to choose from, but a long used and tested is ActiveState Perl. Choose the X_86 version for Windows.
Download and execute the package following the instructions. You can watch this YouTube video to have and idea: the installation process is quite straightforward.
Installing a text editor
Testing Perl
Open a shell terminal. (Under Windows hit Start, then choose “Run…” and type cmd in the text input, then hit Enter).
Type the “perl -v” command, without quotes, and hit enter. Is it working?
Dear students,
welcome to this blog. This is the reference website for the practical course of Genomics, that – as you already know – focuses on genome finishing, both from the bioinformatics side and the wet lab side.
This blog will contain lessons and protocols, but also open questions and polls. A course calendar is online.
Please, register to this blog and start commenting on posts to answer question and – of course – feel free to ask some!
We’ll publish polls from time to time (the first is here, left column!)… We’d love to hear your voice (clicks..)!
Stay tuned,
Andrea & Elisa
PS: Beside this blog we also opened a Wiki, and we’ll tell you how to use it… Consider that the wiki is your open space, and populating it is.. up to you 🙂
