Science October 22nd, 2013 Better sequences (and fewer homopolymer errors) for Ion Torrent The short read files that Ion Torrent’s sequencing machines give us still contain many homopolymer errors: errors in the number of bases called when a single nucleotide occurs more than once in sequence. This makes alignment harder and drowns real indels in a sea of noise. These homopolymer errors arise … Written by Nate Science August 23rd, 2013 A mystery muscle lincRNA We know that our whole genome is distributed to (almost) every cell of our bodies. This fact can be used both to surprise introductory biology students and to usefully refine a fundamental scientific question. Instead of merely asking how it comes to be that different parts of our bodies have … Written by Nate Featured June 25th, 2013 RNA-Seq Interactive Literature Review RNA-Seq is fast becoming the top method for examining the transcriptional activity of genomes. In the five years since the first publications described the technology, RNA-Seq has enabled the discovery of new transcripts in well-studied genomes, challenged our views of imprinting, offered insights into the biology of cancer, and transformed new … Written by Kate Blair Science June 4th, 2013 Short read alignment: seeding In my last post I explained some of the basics of short read alignment algorithms. Go read it if you like; if not, recall that: Many modern alignment algorithms rely on what is called seeding and extending. “Seeding” is finding exact matches of part of the read with part of the … Written by Nate Science April 29th, 2013 Short read alignment: an introduction Biologists today often find themselves with lots of–say, 10^6–short sequences of DNA from a sample, and their ability to do scientifically useful things with those sequences depends on their ability to align those sequences to a reference sequence. Many of the hard and important projects in genomics either are alignment … Written by Nate Featured April 1st, 2013 Unicorn genome sequence announced A landmark genome announcement was made by the Equid Sequencing Consortium today. Scientists hope that the new data will explain origins of the horn and help identify key genes that drive horn development. A high-quality draft of unicorn genome was published today and will be submitted to GenBank later this spring. Written by brandi Science February 5th, 2013 RNA-Seq: The first wave of papers A flurry of papers in May of 2008 introduced the world to RNA-Seq. This new technology provided a higher resolution picture of transcription than was possible ever before. Nearly five years on, we look back at the publications that upset the microarray industry and sent tweed-clad professors scrambling for the … Written by Kate Blair Science August 27th, 2012 Coding with DNA This guy is awesome. He’s coding 3-dimensional shapes with DNA. And substantiates my claim that coding is magic. Written by Kate Blair Science April 27th, 2012 Upside Down Some people are doing what we’re doing in reverse: coding new genomes from scratch. They’re taking out all the natural complexity that our pipelines are built to sort through and are coding “grokkable” genomes that: Read in one direction Are non-overlapping Are as simple as possible Here’s a lovely article about this … Written by Kate Blair Posts navigation 1 … 3 4 5
