Search
Now showing items 1-10 of 10
Quake: quality-aware detection and correction of sequencing errors
(2010-11-29)
We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy ...
Assembly complexity of prokaryotic genomes using short reads
(2010-01-12)
Background: De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the ...
A whole-genome assembly of the domestic cow, Bos taurus
(2009-04-29)
Background: The genome of the domestic cow, Bos taurus, was sequenced using a mixture of
hierarchical and whole-genome shotgun sequencing methods.
Results: We have assembled the 35 million sequence reads and applied a ...
Searching for SNPs with cloud computing
(Springer Nature, 2009-11-20)
As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the ...
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
(Springer Nature, 2008-05-01)
Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of ...
Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus
(Springer Nature, 2007-06-26)
Bracoviruses (BVs), a group of double-stranded DNA viruses with segmented genomes, are mutualistic endosymbionts of parasitoid wasps. Virus particles are replication deficient and are produced only by female wasps from ...
Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera
(Springer Nature, 2010-10-25)
The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understanding of ...
Genome assembly forensics: finding the elusive mis-assembly
(Springer Nature, 2008-03-14)
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation ...
The rise of a digital immune system
(Springer Nature, 2012-07-12)
Driven by million-fold improvements in biotechnology, biology is increasingly shifting towards high-resolution, quantitative approaches to study the molecular dynamics of entire populations. One exciting application enabled ...
Comparative genomics of mutualistic viruses of Glyptapantelesparasitic wasps
(Springer Nature, 2008-12-30)
Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences ...