The Half Decent Pharmaceutical Chemistry Blog

As many adolescences, at the beginning of high school I went through my rebellious period: interested in anarcho socialism and communism, curious about the “No-Global” movement, committed to many social issues such as immigration, pollution, equity, etc. If you are European, there’s a chance you, too, spent a bit of your adolescence dressing up like a squatter, participating in boring meetings and attending endless and pointless conferences.
That was a long time ago, when hormones can make a male teenager go crazy and oddly embark on silly projects for emulation or a physiological need to do something radical and, in his view, shocking.

Although adolescence, like acne, only lasts a few years and, fortunately, (most of) lads grow up from many points of view, this means I’ve turned myself into a globalisation-enthusiast, who likes fast-foods and famous sportswear brands, with no sense of social commitment (whatever that really means). This said, I just want to make clear I hoped Boris Johnson to become the new mayor of London.

However, my political views will be fully discussed in the Euchromatic Blog, as this post is solely about bioinformatics and, in particular, sequence alignment. To be honest, I can’t stand bioinformatics: I hate having to waste time in front of a computer doing BLAST searches on Gene Bank  or fishing for isoforms on Swiss Prot. Even worse, I’m not particularly excited by people who choose to carry out their research sitting at a computer instead of handling pipettes and getting dirty and smelly with media and reagents.

Unfortunately, last year, my current group leader insisted that I had to take a bioinformatics exam. The idea was to make practice with data bases but, sadly, the course annoyed me with depressing lectures on how Google works or the characteristics of an algorithm.
Nevertheless, the bit about sequence alignment was quite interesting. There are two levels of alignment: an algorithm can perform a pair-wise or multiple alignment. For example, BLAST utilises multiple alignments as it compares our target sequence to all the strings present in a data base.
More interesting is the distinction between global and local alignment: with the former you basically align the whole sequence(s), while the latter is based on dividing a string into segments and it is obviously the ideal option for a data base.

A global, pair wise alignment requires gaps in between the 2 sequences in order to obtain the best score. A global, multiple alignment is what you need when trying to predict secondary and tertiary structures.
A multiple, local alignment, on the other hand, aims at the so-called Maximal Segment Pair (that presents the highest matching score).
Therefore, the algorithm performs a multiple alignment, locally matching and retrieving only those with a score above a threshold.

Great stuff when you cannot sleep, eh?

Yesterday, after posting my last message here, I suddenly found myself under the attack of evil forces, that thought, although this is likely to be the oldest computer in the Western world, this was a comfortable place for making some noise.

I like this computer and using it makes me feel proud. It's like an old sport car (like a Jaguar from the Sixties): any one can drive a brand new Mercedes S-class, just a few can live an old convertable, every day, sun, rain or snow.
In order to do it, the machine has to be treated gently and you must know it quite well.

As I said, despite having 64MB of RAM and Pentium III 450MHz, XP works very well: with my DSL connection, I can check the forums on chemicalforums.com, use messenger and listen to one of my MP3s with media player (10th edition, baby!).
There are certainly a few drawbacks: for example, I can't install a recent, decent, anti virus. What I will use, from now on, to protect this old fellow is a free firewall (XP has one, but I wouldn't rely on it too much).
I have to say that, once graduated (2 years), my family (yes, all of them, not only my parents: we are Italian, we are not very rich) will buy me a laptop, since I want to go abroad for a PhD. But this is a different story.

So, yesterday, I was hit by, above all, an enormous number of ad-wares.
I managed (fighting my way through windows constantly popping up) to download a free trial version of Panda Antivirus 2007, install it and run it. A high number of viruses and ad-wares was found. But, as I discovered, the most vicious of them survived.
I tried the Active Scan (over  night, I went to bed at 2am), which, finally, wiped out the viruses (that had increased in number, meanwhile) but can't remove ad/spy-wares: it only tells you where and how many they are.

This morning (woke up at 7) I was really disappointed: before going to the University I tried to manually delete all the files, but couldn't find all of them (c'mon, I didn't have enough time).
However, once at the university, I explained to my friends my problem: they had two different opinions (namely, Ad-Aware and Avast!).
I said that I would have entitled computing guru one of them, according to the outcome.

Well, thing is I opted for a third solution: I reinstalled the free trial but, this time, I updated its files first.
And, this time, it was all nice and smooth! 15 ad-wares detected and destroyed!

Oh, yes, I'm so proud of my old-fashioned sport coupé!

By the way, after a promising start, Chemblogs, now, looks like an abandoned building, with three or four people living in. It reminds me the final, well-known, scene of Blade Runner.
I hope Mitch will NOT think about shutting everything down: I really like writing a blog.