Next Gen Sequencing (NGS) and Bioinformatics at UVic
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Key recombination gene in higher mammals - PRDM9

Key recombination gene in higher mammals - PRDM9 | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

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
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BG7, a new system for bacterial genome annotation designed for NGS ...

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 ...)...
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The Tree of Life: Elaine Mardis rocks: nice talk on "Next generation sequencing"

The Tree of Life: Elaine Mardis rocks: nice talk on "Next generation sequencing" | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
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RefSeqGene tutorial (video)

An overview and tutorial about RefSeqGene, a resource at NCBI that is the standard for reporting gene-specific sequence variation.
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O|B|F News | Open Source Bioinformatics news

O|B|F News | Open Source Bioinformatics news | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

Via Mohamed Nadhir Djekidel
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The Galaxy Project: Online bioinformatics analysis for everyone

The Galaxy Project: Online bioinformatics analysis for everyone | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

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
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Turning off Small RNA: Michigan Tech Scientist Designs a New Tool for Breaking the Epigenetic Code | Michigan Tech News

Turning off Small RNA: Michigan Tech Scientist Designs a New Tool for Breaking the Epigenetic Code | Michigan Tech News | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
A single  strand of small RNA can play a big role.
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RDP home page

RDP home page | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

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
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Metassembler: Improving de novo genome assembly

Found on Twitter:  bit.ly/wt6Uv2 #agbt  Links to a PDF

Metassembler: Improving de novo genome assembly
Paul Baranay, Scott Emrich, Michael Schatz

 

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PLoS Collections: A Quick Guide for Developing Effective Bioinformatics Programming Skills

"The following set of guidelines distill several key principals of effective bioinformatics programming, which the authors learned through insights gained across many years of combined experience developing popular bioinformatics software applications and database systems in both academic and commercial settings.."


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Web services for bioinformatics, Part 1

This series describes the process of building, deploying, and using high-throughput web services for bioinformatics applications.

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Genome Sequencing Finds Unknown Cause of Epilepsy | UANews.org

Genome Sequencing Finds Unknown Cause of Epilepsy | UANews.org | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

UA researchers have identified a previously unknown mutation in a sodium channel protein as the likely cause of a severe form of epilepsy.

(University of Arizona)

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Introduction to Circos, Features and Uses // CIRCOS Circular Genome Data Visualization

Introduction to Circos, Features and Uses // CIRCOS Circular Genome Data Visualization | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

Circos is flexible. Although originally designed for visualizing genomic data, it can create figures from data in any field. If you have data that describes relationships or multi-layered annotations of one or more scales, Circos is for you.

Circos can be automated. It is controlled by plain-text configuration files, which makes it easily incorporated into data acquisition, analysis and reporting pipelines (a data pipeline is a multi-step process in which data is analyzed by multiple and typically independent tools, each passing their output as the input to the next step).


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Download Folding@home!

Download Folding@home! | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
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
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Computer Scientists' Solution to a Biologist’s Problem - Bio-IT World

Computer Scientists' Solution to a Biologist’s Problem - Bio-IT World | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
RT @druvus: Computer Scientists' Solution to a Biologist’s Problem http://t.co/62bzZgVZ #bioinformatics #populus...

 

Database searching...

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PLoS ONE: A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

PLoS ONE: A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

"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...."


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Marion Koopmans's curator insight, February 16, 2013 11:13 AM

lots of comparisons needed, but hard to keep up!

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BLAST 2.2.26+ release. Basic Local Alignment Search Tool

BLAST 2.2.26+ release. Basic Local Alignment Search Tool | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

BLAST 2.2.26+ release.

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The Genome Question - What Do We Have In Common With A Gorilla?

The Genome Question - What Do We Have In Common With A Gorilla? | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
Researchers have completed the genome sequence for the gorilla, the last genus of the living great apes to have its genome decoded.
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Microbial Informatics and Experimentation | Abstract | Metagenomics - a guide from sampling to data analysis

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms.
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NCBI BLAST on Windows Azure - Microsoft Research

NCBI BLAST on Windows Azure - Microsoft Research | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
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...

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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

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Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques | Science Codex

Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques | Science Codex | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
Analyzing complex plant genomes with the newest next-generation DNA sequencing ... - Science Codex: Science Code...
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Challenges of sequencing human genomes

Massively parallel sequencing technologies continue to alter the study of human genetics. As the cost of sequencing declines, next-generation sequencing (NGS) instruments and datasets will become increasingly accessible to the wider research community. Investigators are understandably eager to harness the power of these new technologies. Sequencing human genomes on these platforms, however, presents numerous production and bioinformatics challenges. Production issues like sample contamination, library chimaeras and variable run quality have become increasingly problematic in the transition from technology development lab to production floor. Analysis of NGS data, too, remains challenging, particularly given the short-read lengths (35–250 bp) and sheer volume of data. The development of streamlined, highly automated pipelines for data analysis is critical for transition from technology adoption to accelerated research and publication. This review aims to describe the state of current NGS technologies, as well as the strategies that enable NGS users to characterize the full spectrum of DNA sequence variation in humans.


Via Mohamed Nadhir Djekidel
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My Weblog on Bioinformatics, Genome Science, Next Generation ...

My Weblog on Bioinformatics, Genome Science, Next Generation ... | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it
... actual data. I totally agree with his point about not making the same mistake with the other laggards in seq tech especially when I think in sequencing the bioinformatics (or data analysis ) will make or break the platform.
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Google Invests in Bioinformatics: DNAnexus CEO, Andreas Sundquist | mendelspod.com

Google Invests in Bioinformatics: DNAnexus CEO, Andreas Sundquist | mendelspod.com | Next Gen Sequencing (NGS) and Bioinformatics at UVic | Scoop.it

Andreas Sundquist is here to talk about his exciting new company. He’s the CEO and co-founder of DNAnexus, a company receiving a fair amount of buzz since catching a chunk of cash from Google Ventures and TPG Biotech.

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