Now showing items 1-10 of 13
Quake: quality-aware detection and correction of sequencing errors
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 ...
Clustering metagenomic sequences with interpolated Markov models
Background: Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because ...
Detection and correction of false segmental duplications caused by genome mis-assembly
Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental ...
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
Background: Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray ...
A whole-genome assembly of the domestic cow, Bos taurus
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 ...
Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
(Springer Nature, 2011-05-31)
Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). ...
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 ...
Between a chicken and a grape: estimating the number of human genes
(Springer Nature, 2010-05-05)
Many people expected the question 'How many genes in the human genome?' to be resolved with the publication of the genome sequence in 2001, but estimates continue to fluctuate.
Genome re-annotation: a wiki solution?
(Springer Nature, 2007-02-01)
The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated ...
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 ...