Bioinformatics or B101nformatics

Do you ever heard about hexamer likelihood used to determine if a sequence is coding or not? In one of my assigments on my master of Bioinformatics there was a project to use hexamers instead. The hexamers are defined with 6 nucleotides on a sequence. The idea behind using hexamers is considering that in coding regions there is an influence of the previous codon to the next codon, whereas on the intronic or non-coding regions there isn't. The script works need three fasta files, the first one with intronic sequences, the second one with coding sequences, and the last one with sequences to analyze. All files must use the IUPAC code for sequences, and on the right frame. This is due to the way of signaling in which frame a sequence should be, which varies between programs and descriptions. It is also more difficult to calculate the best score for the unknown sequence, without presenting two scores or biasing for a training set. Assuming everything is on frame is safer and easi...

I'm sorry this month the news post will come with some delay, but there will be another post with it. If you like potatoes take one:

Now again I want to share with you some news: Novel online bioinformatics tool significantly reduces time of multiple genome analysis Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins In the First Bioinformatics Hackathon, Computer Scientists Meeting in Russia Use their Computer Skills to Fight Deadly Diseases Chemicals giant DuPont buying Taxon Biosciences MarkerMiner 1.0: An easy-to-use bioinformatics platform for DNA analysis in angiosperms New 3-D Method Improves the Study of Proteins OpGen raises $17 million in initial public offering , to develops tests to help hospitals identify drug-resistant bacteria  Massively parallel biology students: More than 900 students co-author genomics research paper , an interessting effort to do science Researchers obtain precise estimates of the epigenetic mutation rate BIB logo of their website. And last but not least, there was the announcement from the BIB of a n...

To improve my Bioinformatics report, I started using a couple of tools. I tried to include the page with less ads when possible, if you find any source too crowded with ads please let me know: Genome Canada Launches C$30.5M Genomics Innovation Network and makes  $24M pivo t to bolster bioinformatics capabilities Genenentech search for bioinformatic  chief after Robert   Gentleman leaves for 23andMe Appistry extends its tools and services for analyzing Next-Generation Sequencing data with GenomePilotNIAID-led partnership seeks to establish bioinformatics centers in Africa Curoverse announces new infrastructure software for precision medicine, genomics and bioinformatics : A beta of cloud and on-premise solutions for organizations and individuals using the new Arvados open source software platform to manage, process, and share genomic and biomedical data is now public Sequences onlline Discover the global bioinformatics market 2020 due to the increase...

I must confess this month I thought I had any new to share but right after I published last post I found one which I saved for this month: The first epigenomic's map:( Spanish,   English) The logo of the consortium ( Roadmap Epigenomics Mapping Consortium )  involved on the Epigenomic's roadmap Sometimes people complain that bioinformaticians think that a gene is defined by a position in a chromosome or a genetic element, plasmid, mitochondrial chromosome, genome... I don't think so, many bioinformaticians are biologist who know how replication, transcription, and translation works molecularly. However the easiest way to work with genomes implies omitting it, and work with known sequences and suppose that they are transcribed and translated literally. With this step and the previously know Encode project we learn more about splicing and epigenomics and in the future we will see how this will change bioinformatics work.