My personal and professional adventure into Science

Archives for August 2013

Relaxing in Vienna

After only having one week of vacation since I visited Australia in February, I decided to take some days off. I am now in Vienna where I will visit two friends I met at a summer school in Lipari 3-4 years ago. My main holiday will still be saved for a winter vacation somewhere warmer than Denmark, or colder for that sakes if it includes a lot of ice, snow and mountains 🙂

The last weeks have been tough, or months for that sakes, lots of work work work and Monday + Tuesday, Henrik and I had 14 oral re-exams with students attending our Introduction to Bioinformatics course. It was sad to see that only 55% of the students passed this year vs. 80% last year. Same teachers, lectures, exercises and TA’s. Only difference was the students. This down going trend in passing was unfortunately also seen in other courses. I hope next year will be better 🙂

To quickly recharge, I found a nice hotel with a lot of relaxation options, if that is what I want. Most preferably I would have liked to take a week or two to a warmer country with nice beaches, cold drinks and a lot of nature to explore. Unfortunately this just didn’t fit my schedule now, so that will be later, and it will also be nice to catchup with Marta and Paweł 🙂

The hotel I found has a spa with whirlpool, steam bath, sauna, pool, massage and a gym. And also a strange thing called an Alphalounger. It looks weird, but apparently it should recharge your mind, body and soul. I will see if it works 🙂
So, there should be plenty of opportunities to recharge if the weather turns bad.

Fortunately weather is nice, it’s around 22-23 degrees and sunny. So I think I will continue exploring the city and see what I can find 🙂

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New method for identifying genotype-phenotype correlations in protein multiple sequence alignments

At my office we are four people working in three different groups. Edita and Leon work in the Immunological Bioinformatics group, Mette is in the Integrative Systems Biology besides being a guest member of Functional Human Variation, and I work in the Metagenomics group and is also a guest member of Functional Human Variation. The variation of research areas make our discussions really funny sometimes because our areas are so different. They often find it funny when I talk about my DNA from horses, zebras, quagga, giant squid, polar bear or other weird animals and/or species 🙂

Recently Leon published a paper for a project he has worked hard on for some time now, the relief was very visible in Leon’s face when it finally came online 🙂

The paper is describing a webserver named SigniSite, abstract is below.

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Identifying which mutation(s) within a given genotype is responsible for an observable phenotype is important in many aspects of molecular biology. Here, we present SigniSite, an online application for subgroup-free residue-level genotype–phenotype correlation. In contrast to similar methods, SigniSite does not require any pre-definition of subgroups or binary classification. Input is a set of protein sequences where each sequence has an associated real number, quantifying a given phenotype. SigniSite will then identify which amino acid residues are significantly associated with the data set phenotype. As output, SigniSite displays a sequence logo, depicting the strength of the phenotype association of each residue and a heat-map identifying ‘hot’ or ‘cold’ regions. SigniSite was benchmarked against SPEER, a state-of-the-art method for the prediction of specificity determining positions (SDP) using a set of human immunodeficiency virus protease-inhibitor genotype–phenotype data and corresponding resistance mutation scores from the Stanford University HIV Drug Resistance Database, and a data set of protein families with experimentally annotated SDPs. For both data sets, SigniSite was found to outperform SPEER.
SigniSite is available at: http://www.cbs.dtu.dk/services/SigniSite/.

 

http://nar.oxfordjournals.org/content/41/W1/W286.abstract

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