Blog posts

2017

2016

miRNA Annotation Tools Comparison

3 minute read

Published:

In summary: I will show which is the best miRNA mapping tool. I used several options for this benchmarking:

2013

small RNA abundance [miss-] viz

1 minute read

Published:

My PhD was focused on small RNA sequencing data. I had a problem when I wanted to visualized the amount of small RNAs from the beginning. Here the problem, assume that you have a certain distribution of small RNA sequences abundance:

miRNA annotation: complex scenarios

4 minute read

Published:

Everybody who is working with microRNA knows about miRBase, it was the first miRNA catalogue. Everybody is using it to annotate small RNA sequences as miRNA or not. And it is great, and very helpfully…but there are some cases that we should investigate our results.

2012

visualizing small RNA mapping complexity

1 minute read

Published:

I spent all my PhD working with small RNA sequences data. The main problem was, always those sequences that map in multiple locations, also denominated ambiguous sequences. From the very beginning, this made that pipelines remove this kind of sequences from the analysis, because you cannot assign them a unique location in the genome. But these sequences are interesting to study, since many of them change in size, for instance. This complexity is due to repeats in the genome and the scenario I am talking about here it is shown in the following figure:

Visualizing science is also cool @polychart

1 minute read

Published:

One of my interest in science is finding new ways to visualize Big Data. Scientist are used to work with static visualization, that of course, is wonderful in the majority of the case. But it wouldn’t be better dynamic visualization for exploration? Play with your data, explore, and finally when you get that great figure that tell you everything you was looking for, you can export it to an image portable format.

Bionformatics evolution 2005-2012

less than 1 minute read

Published:

How much keywords in bioinformatics has changed in the past 7 years?
I did a small and quick experiment. I took the abstract of the papers published in Bioinformatics during Jan-2005 and during Jan-2012. Then I represented the words according to their frequency with the wordle tool. And the result was: