link
Not a plug for LC Sciences, but they do have a comprehensive web resource list for miRNA related info.
Not a plug for LC Sciences, but they do have a comprehensive web resource list for miRNA related info.
Monday, 31 January 2011
Saturday, 29 January 2011
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.
URL above links to tutorial for use to generate a 3 way venn diagram.
Friday, 28 January 2011
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 3rd-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.”
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 3rd-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.
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."
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."
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