ademcan's blog

A "shiny" spliceosome

06/01/2013 - No comments

Today, I designed a "shiny" spliceosome using Photoshop. Look how beautiful it is smile

Legend:

the two red rectangles represent the exons
GU and AG are the nucleotides defining the start and end position of the intron
BPS : Branch Point Sequence
(Py)n : Polypyrimidine tract
ESE : Exonic Splicing Enhancer
ESS : Exonic Splicing Silencer
hnRNP : heterogeneous nuclear RiboNucleoProteins
U+number : different sub-units of the spliceosome
SR proteins : Serine (S) Arginine (R) rich proteins

You can find this picture at:
http://ademcan.net/docs/images/spliceosome/spliceosome.jpg
Feel free to use it in your projects.
Credits: ademcan

UPDATE: If you want to modify the image, you can use the .psd file in Photoshop
http://www.ademcan.net/docs/images/spliceosome/spliceosome.psd

Tags : Bioinfo

Poster prize at ECCB12 with my augmented reality poster

13/09/2012 - 3 comments

UPDATE: you can find the video online here, thanks to Yoann (Moussor) from bioinfo-fr.net for the video.

Yesterday I got the 1st rank poster prize at the ECCB12 (European Conference on Computational Biology 2012) conference in Basel Switzerland. I am very happy and I really hope to see more and more posters with AR in the future. I would like to thank all my friends for their support and also Henrik Kaessmann and Anamaria Necsulea my PhD supervisors.
Here is a picture of the result: (for people wondering where is the AR on the poster, I have the same target image on my poster but this one was next to my poster to let people play with it).
The 3D object represents two exons (red) and one internal intron (black and white) which recrute the different sub-units of the spliceosome (U1,U2,U4,U5,U6)

arposter

I will write a post with all the details on how to create an AR app for iOS using the Qualcomm Vuforia SDK, Unity3D and xCode ASAP...
And if you see any post or info related to my poster I would love to also read it, feel free to send me the link, thank you smile .

Tags : Bioinfo

Sequence your own genome using a USB stick

22/02/2012 - No comments

     Sequencing became easier nowadays thanks to the high-throughput (or next-generation) sequencing. With these new sequencing methods, a single genome can be sequenced within few days or hours, depending on how big the genome is. This very powerful and high quality technology is based on the parallelization of the sequencing process generating millions of sequences at once. Thanks to the generalization of these methods, the prices were also pulled down but remains still expensive and not for individual use.
     Nanopore Technologies is a company based in Oxford and active on the sequencing area. Last week during the Advances in Genome Biology and Technology conference, Oxford Nanopore Technologies presented a new product to sequence any genome very rapidly and at a lower price. This module is named minION and presented as a simple USB stick. To sequence a genome, any sample such as blood or plasma should be enough. The sequencing will take place within the USB stick and the results available on your computer. A number of tools are provided to work on the newly sequenced genome.
     The sequencing protocol is based on a nanopore mechanism. A nanopore is a small hole (blue element on the picture) found in many cellular membranes. Depending on the pore, it allows some molecules to pass and blocks some others. Two methods are available for the nanopore based sequencing: the strand sequencing and the exonuclease sequencing.
     In strand sequencing, the nanopore will be coupled with an enzyme (green element on the picture) linked to the dna. The enzyme will open the double-stranded DNA and direct it through the nanopore. In exonuclease sequencing, the system is very similar. The DNA molecule is attached to the nanopore by the exonuclease which cleaves the DNA to single nucleotides passing through the nanopore. Each element passing the nanopore is analyzed, and a different signal specific to each nucleotides A, C, T or G is produced.
     At the end we obtain a whole sequence of signals translated to the corresponding DNA sequence. As an example, the researchers sequenced the genome of the PhiX virus composed by 5000 based pairs in few minutes. This technology can be used in medicine to quickly detect a genetic related disease for example or detection of viruses. The nanopore sensing works also with RNA, proteins and other small molecules. The product will be available soon for a price around 900 $.
     However, some points still need to be clarified. For example the minION should be for a unique run, which will results in higher price for multiple samples studies. Another point is about the quality. Actually the minION cannot sequence at a single-base sensitivity, the nanopore is reading three bases at a time and an algorithm is used to define the best matching sequence. The company announced that they are hardly working on trying to get a single-base sensitivity.
     As I mentioned, the minION still needs some improvements, but we can easily say that we are rapidly coming to a very-high-throughput-next-generation sequencing.

credits: piture from nanoporetech.com

Tags : Bioinfo