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Guest curators: Nik Veldhoen Ed Rybicki (U of Cape Town; http://bit.ly/wYBezD) Visit Ed's Scoop.it: http://www.scoop.it/t/virology-news
The analysis of next-generation sequencing data from large genomes is a timely research topic. Sequencers are producing billions of short sequence fragments from newly sequenced organisms. Special Issue of Briefings in Functional Genomics 
Researchers from Karlsruhe Institute of Technology (KIT) in Germany and the National Tsing Hua University in Taiwan have created a DNA-based (Salmon DNA-based memory device | KurzweilAI http://t.co/utx6zx9R... Via Dr Richard Badge 
Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals. Via Mohamed Nadhir Djekidel 
RT @druvus: Computer Scientists' Solution to a Biologist’s Problem http://t.co/62bzZgVZ #bioinformatics #populus...
Database searching... 
"he advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform...." Via Mohamed Nadhir Djekidel 
BLAST 2.2.26+ release. 
Researchers have completed the genome sequence for the gorilla, the last genus of the living great apes to have its genome decoded. Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. 
Built on Windows Azure, NCBI BLAST on Windows Azure is a cloud-based implementation of the Basic Local Alignment Search Tool (BLAST) that enables researchers to take advantage of the scalability of the Windows Azure platform to perform analysis of... Via Mohamed Nadhir Djekidel
bffo RT @galaxyproject: Tool Shed - lots of good stuff
Found on Twitter: bffo RT @galaxyproject: Tool Shed: SCALCE: Tool for compression of FASTQ files; bit.ly/gxyshed #usegalaxy #bioinformatics 
Analyzing complex plant genomes with the newest next-generation DNA sequencing ... - Science Codex: Science Code... |
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ.
Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Via iMicroBham 
The results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case–control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors.
Three original papers are here: http://www.nature.com/nature/index.html Via Dr. Stefan Gruenwald 
The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) Via Mohamed Nadhir Djekidel Epigenetic Modifications To DNA Caused By Exercise (Medical News Today): Share With Friends: | | Top News - He... Via Dr Richard Badge 
PRDM9 has evolved exceptionally rapidly between humans and chimpanzees and this rapid evolution explains a second, previously published, finding of the researchers: recombination hotspots also differ between humans and chimpanzees. Remarkably, PRDM9 is involved not just in determining mouse hotspot locations, but is also a key player in mouse speciation. Via Dr. Stefan Gruenwald Slides from the talk presented at the conference "Applied Bioinformatics and Public Health" at Cambridge during 1-3 June 2011 (BG7, open-source (AGPL) bacterial genome annotation pipeline system for NGS, from #ohnosequences ...)... An overview and tutorial about RefSeqGene, a resource at NCBI that is the standard for reporting gene-specific sequence variation. 
orm, reproduce, and share complete analyses. The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University. The Galaxy Project is supported in part by NSF, NHGRI, The Huck Institutes of the Life Sciences, The Institute for CyberScience at Penn State, and Emory University. Via Mohamed Nadhir Djekidel 
A single strand of small RNA can play a big role. 
Recombination Detection Program (RDP) RDP applies a number of recombination detection and analysis algorithms. It runs under Windows 95/98/NT/XP/VISTA/7. You may download: the most up to date (but still unstable) version of the program (RDP4 Beta 4.14 including VB runtimes, accessory apps, LDHat lookup tables and a large 3Seq p-value lookup table)the full program (smaller download) (RDP3 Alpha 44 including VB runtimes, accesory apps & LDHat lookup tables)the full program (bigger download) (RDP3 Alpha 44 including VB runtimes, accesory apps, LDHat lookup tables and a large 3Seq p-value lookup table)a user manual
Screenshot courtesy of "Contagion" - which used it without credits Via Ed Rybicki
Metassembler: Improving de novo genome assembly
Found on Twitter: bit.ly/wt6Uv2 #agbt Links to a PDF Metassembler: Improving de novo genome assembly
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