miRNA web resources @ LC sciences

link
Not a plug for LC Sciences, but they do have a comprehensive web resource list for miRNA related info.

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizable, high-resolution Venn and Euler diagrams in the R statistical environment. To fill this gap we introduce VennDiagram, an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams with up to three sets.

HiSeq doubles its output, a next-gen sequencing primer, and return of genetic

Excellent summary post over at genomes unzipped. Hate blogging from iPhone. Anyway URL in topic title.

Pybedtools - python wrapper for bedtools

Looks interesting!
URL above links to tutorial for use to generate a 3 way venn diagram.

Pacific Biosciences Team Identifies Asian Origin for Haitian Cholera Bug

Rising importance of NGS for emerging infectious diseases!
excerpted from Bio-ITworld URL above

December 9, 2010 | In a dramatic piece of ultra-quick genetic detective work, next-generation sequencing company Pacific Biosciences has decoded the sequence of the strain of bacteria responsible for the deadly cholera outbreak in Haiti. The findings, which confirm the putative Asian origin for the devastating disease, are published online in the New England Journal of Medicine today. 
....

Each of the five strains took about one day to sequence to about 60X coverage. “They did an outstanding job in the analysis,” says Waldor. “Most of the credit for this project goes to Eric and his team.”  
“The rapidity and depth of the sequence using this 3^rd-generation sequencing technology has enormous potential to transform how we can analyze outbreaks of infectious disease and even the prediction of future outbreaks because of the power of their technology.” 
According to PacBio, the five cholera genomes were sequenced on November 12 to 12-15X coverage in less than two hours. Further runs bumped up the coverage to 60X over the course of the day. Over the next three days, the sequence data were subjected to in-depth analysis, including genome assembly, annotation, and sequence comparisons, including comparisons to nearly two dozen published cholera genomes.  
...
From PacBio’s perspective, Schadt says that “real-time monitoring” of pathogens opens the door to using his firm’s technology as “a routine surveillance method, for public health protection in addition to pandemic prevention and response.” 

5AM Rolls Out Free Firefox Plugin that Connects Personal Genomic Information to External Content

Social Media and Personal genomics!
let's wait for the facebook app or maybe Flock integration

The plugin, dubbed SNPTips, allows users to compare their 23andMe raw genetic information with SNP data from publicly available resources, such as databases and journal articles.

Broad Institute Designs Protocols to Sequence HLA Regions from up to 95 Individuals on 454 Platform

Fascinating! I wonder if the protocol is shared. Anyone has it?
Excerpted from genomeweb. URL above
"The protocols enable up to 95 samples to be pooled, resulting in a cost of around $40 per sample, including the cost of reagents, labor, and equipment. The researchers are now using their protocol to sequence the HLA regions of 3,000 HIV-positive individuals."

Beyond the Genome conference

Genome Biology, in conjunction with Genome Medicine, is pleased to host the second annual Beyond the Genome conference in Washington DC from 19 - 22 September 2011. This year’s conference will focus on cancer genomics, the human microbiome and exome and genomic sequencing and how these approaches are being used to identify common and rare disease-causing mutations. Technological as well as medical or biological perspectives will be discussed.

DNAvision offers Human WGS for 7,500 euros

I had imagined exome sequencing would still have a good run for the next 2-3 years but seeing how commercial service providers are throwing caution to the wind and offering Whole genome sequencing at ever decreasing costs, I think many will soon revert to WGS instead. Exome sequencing kits will have a lot to catch up in terms of price and useful data if they are to match up with quickly plummeting WGS prices.
DNAVision to Offer $10K Human Genome Sequencing Services; Purchases Four SOLiDs
Landed: First Illumina HiSeq Machines Advertised (By Nick Loman on February 10, 2010)

The $1,000 Genome Debate is 'Already ... Irrelevant'

excerpted from GenomeWeb
Matthew Herper and Daniel MacArthur are at odds over the $1,000 genome. Forbes' Herper argues that even though sequencing is becoming cheaper, analyzing a genome still costs much more than $1,000. Over at Genetic Future, MacArthur responds that as sequencing costs continue to fall, "a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools." 

My thoughts on this later.. 

Bioinformatics. 2011 Jan 7. [Epub ahead of print]

A fast, lock-free approach for efficient parallel counting ofoccurrences of k-mers.

Marçais G, Kingsford C.

Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland, College Park, MD, USA.

Abstract

MOTIVATION: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment, and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multi-core computers have become commonplace in research facilities allowing for a new parallel computational paradigm.

RESULTS: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multi-threaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory efficient solution.

AVAILABILITY: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.

CONTACT: gmarcais@umd.edu.

PMID: 21217122 [PubMed - as supplied by publisher]

Cell. 2011 Jan 7;144(1):27-40.

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development.

Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP,Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, Campbell PJ.

Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

Abstract

Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer. PAPERCLIP:

Copyright © 2011 Elsevier Inc. All rights reserved.

PMID: 21215367 [PubMed - in process]

AGBT Meeting is Sold out!!

Not attending the 2011 AGBT but am curious about the speakers. Was surprised to find that the meeting is sold out!
http://agbt.org/

I guess Sequencing and Genomics is all the prime focus now in Biology and everyone is interested to find new applications or produce reagents for high throughput sequencing.

Search and clustering orders of magnitude faster than BLAST, Bioinformatics.

Hmmm must check out this... Edgar, R.C. (2010), Search and clustering orders of magnitude faster than BLAST, Bioinformatics.
doi: 10.1093/bioinformatics/btq461
http://www.drive5.com/usearch/usearch_docs.html