Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads

In this paper, we introduce a novel hierarchical genome assembly (HGA) methodology that takes further advantage of such very high coverage by independently assembling disjoint subsets of reads, combining assemblies of the subsets, and finally re-assembling the combined contigs along with the original reads.
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Universal Pacemaker of Genome #Evolution

Universal Pacemaker of Genome #Evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Sagi Snir, Yuri I. Wolf, Eugene V. Koonin

 

A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome.

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The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Bananas (Musa spp.), including dessert and cooking types, are giant
perennial monocotyledonous herbs of the order Zingiberales, a
sister group to the well-studied Poales, which include cereals.
Bananas are vital for food security in many tropical and subtropical
countries and the most popular fruit in industrialized countries1.

 


Via Biswapriya Biswavas Misra
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Stickleback genomes reveal path of evolution : Nature News & Comment

Scientists have pinpointed mutations that may help a tiny armoured fish to evolve quickly between saltwater and freshwater forms.

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Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus : Nature Communications : Nature Publishing Group

Although genome segmentation provides advantages such as genetic reassortment, which contributes to the emergence of novel strains with pandemic potential, it complicates the genome packaging of progeny virions.

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RDP home page

RDP home page | Viruses and Bioinformatics from Virology.uvic.ca | 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

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Cracking the epigenetic code

Cracking the epigenetic code | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A team of researchers at The Australian National University is one step closer to better understanding how organisms function after discovering how epigenetic information is transmitted from one generation of cells to the next.


Via Integrated DNA Technologies
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Genome-Scale Phylogeny of the Alphavirus Genus Suggests a Marine Origin

Using full-length sequences of all known alphaviruses, we produced a robust and comprehensive phylogeny of the Alphavirus genus, presenting a more complete evolutionary history of these viruses compared to previous studies based on partial sequences. Our phylogeny suggests the origin of the alphaviruses occurred in the southern oceans and spread equally through the Old and New World. Since lice appear to be involved in aquatic alphavirus transmission, it is possible that we are missing a louse-borne branch of the alphaviruses.

 

Of course, I think ALL viruses came out of the water - some longer ago than others.  Always thought that was a lousy branch of virology...thanks Stephen Korsman!


Via Ed Rybicki
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A world within a tumour – new study shows just how complex cancer can be

A world within a tumour – new study shows just how complex cancer can be | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Cancer is a puzzle of staggering complexity. Every move towards a solution seems to reveal yet another layer of mystery. For a start, cancer isn’t a single disease, so we can dispense with the idea of a single “cure”. There are over 200 different types, each with their own individual quirks. Even for a single type – say, breast cancer – there can be many different sub-types that demand different treatments. Even within a single subtype, one patient’s tumour can be very different from another’s. They could both have very different sets of mutated genes, which can affect their prognosis and which drugs they should take.


Via Dr. Stefan Gruenwald
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TWiV 152: Viromes in the effluence of society

TWiV 152: Viromes in the effluence of society | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Vincent, Alan, and Rich cover the virome of raw sewage, and a baculovirus gene that causes caterpillars to climb to their doom (TWiV 152: Viromes in the effluence of society http://t.co/qfW9qeDD...)...
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