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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Biostars - Bioinformatics Explained

Biostars - Bioinformatics Explained | Virology and Bioinformatics from Virology.ca | Scoop.it

Tutorials and Q+A Forum for bioinformatic tools. 17 000 + users!

Kathleen McLeod's insight:

Could be an interesting resource!

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Video Tip of the Week: MEGA, Molecular Evolutionary Genetics Analysis | The OpenHelix Blog

This week's tip of the week highlights the MEGA tools--MEGA is a collection of tools that perform Molecular Evolutionary Genetics Analysis. MEGA tools are not
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How A Computer Algorithm Predicted West Africa's Ebola Outbreak Before It Was Announced

How A Computer Algorithm Predicted West Africa's Ebola Outbreak Before It Was Announced | Virology and Bioinformatics from Virology.ca | Scoop.it
The Ebola outbreak in West Africa is focusing a spotlight on a unique online tool run by experts in Boston that flagged a "mystery hemorrhagic fever" in forested areas of southeastern Guinea nine d...
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Samuel Viana's curator insight, August 15, 2014 2:53 PM

Um interessante algoritmo que combina fontes noticiosas, relativamente à frequência de notícias sobre surtos e à proveniência desses mesmos surtos, ajuda a prever a possibilidade de evolução de potenciais pandemias, antes de estas poderem escalar para níveis incontroláveis.

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A Review of “Bioinformatics Algorithms – An Active Learning ...

A Review of “Bioinformatics Algorithms – An Active Learning ... | Virology and Bioinformatics from Virology.ca | Scoop.it
Each chapter attempts to answer a biological/bioinformatics question, but also has multiple sub-themes for students from different backgrounds. The chapters are so elegantly planned that readers from different backgrounds ...
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Bioinformatics for Beginners!

Documenting my Experience Learning Bioinformatics from the Almost Begining
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BMC Bioinformatics | Full text | Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome.

 

The new features of Metavir 2 allow users to explore and analyze viromes composed of raw reads or assembled fragments through a set of adapted tools and a user-friendly interface.

 

http://metavir-meb.univ-bpclermont.fr/

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TeselaGen Is Building A Platform For Rapid Prototyping in Synthetic Biology | TechCrunch

TeselaGen Is Building A Platform For Rapid Prototyping in Synthetic Biology | TechCrunch | Virology and Bioinformatics from Virology.ca | Scoop.it
As the costs of DNA sequencing and synthesis drop precipitously, a host of computer science-meets-biotech startups are cropping up in Silicon Valley...
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BMC Bioinformatics | Abstract | Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results.
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BMC Bioinformatics >> Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

Most proteins have evolved in specific cellular compartments that limit their functions and potential interactions.
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BioJS: an open source JavaScript framework for biological data visualization

BioJS: an open source JavaScript framework for biological data visualization | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary: BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community.

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Bioinformatics Knowledge Vital to Careers | The Scientist Magazine®

Bioinformatics is growing up. Science's hottest information tool is coming into adolescence and has transformed the way research is conducted.

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DSK: k-mer counting with very low memory usage

DSK: k-mer counting with very low memory usage | Virology and Bioinformatics from Virology.ca | Scoop.it
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Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of distinct k-mers to count.

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BMC Bioinformatics | Full text | Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome.
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ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach

Obtaining an accurate sequence alignment is fundamental for consistently analyzing biological data. Although this problem may be efficiently solved when only two sequences are considered, the exact inference of the optimal alignment easily gets computationally intractable for the multiple sequence alignment case. To cope with the high computational expenses, approximate heuristic methods have been proposed that address the problem indirectly by progressively aligning the sequences in pairs according to their relatedness. These methods however are not flexible to change the alignment of an already aligned group of sequences in the view of new data, resulting thus in compromises on the quality of the deriving alignment. In this paper we present ReformAlign, a novel meta-alignment approach that may significantly improve on the quality of the deriving alignments from popular aligners. We call ReformAlign a meta-aligner as it requires an initial alignment, for which a variety of alignment programs can be used. The main idea behind ReformAlign is quite straightforward: at first, an existing alignment is used to construct a standard profile which summarizes the initial alignment and then all sequences are individually re-aligned against the formed profile. From each sequence-profile comparison, the alignment of each sequence against the profile is recorded and the final alignment is indirectly inferred by merging all the individual sub-alignments into a unified set. The employment of ReformAlign may often result in alignments which are significantly more accurate than the starting alignments.
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BLASTing Off – How BLAST Works

BLASTing Off – How BLAST Works | Virology and Bioinformatics from Virology.ca | Scoop.it
More than a pun on the explosive growth of sequencing data, BLAST makes annotation and comparisons of similar sequences much easier. Created by a group at the U.S. National Center for Biotechnology Information in…
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Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online

Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online | Virology and Bioinformatics from Virology.ca | Scoop.it
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A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences

A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access (Guide to #Genomics and #Bioinformatics Training for Clinical and Public Audiences http://t.co/MYOavdN6af http://t.co/iQEp66A7rR)...

Via HaBIc, Alberto Goldoni
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Bioinformatician's Pocket Reference !!

Bioinformatician's Pocket Reference !! | Virology and Bioinformatics from Virology.ca | Scoop.it
  It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special cir...
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Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Links to Recombinant Software Detection/Analysis Software

Welcome to the comprehensive list of recombination analysis software maintained by the Robertson Lab.

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BMC Bioinformatics >> Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering

The structured organization of cells in the brain plays a key role in its functional efficiency.
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BMC Bioinformatics | Base calling for high-throughput short-read sequencing: dynamic programming solutions

Background Next-generation DNA sequencing platforms are capable of generating millions of reads in a matter of days at rapidly reducing costs.
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BMC Bioinformatics | Abstract | GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures

All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less.
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