Detecting horizontal gene transfer by mapping sequencing reads across species boundaries
We present Daisy, a novel mapping-based tool for HGT detection. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy successfully detects HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data.
Availability and Implementation: Daisy is freely available from http://github.com/ktrappe/daisy.
Contact: renardb@rki.de
Supplementary information:...
Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Trappe, K., Marschall, T., Renard, B. Y. Tags: GENES Source Type: research
Pathway-based approach using hierarchical components of collapsed rare variants
Motivation: To address ‘missing heritability’ issue, many statistical methods for pathway-based analyses using rare variants have been proposed to analyze pathways individually. However, neglecting correlations between multiple pathways can result in misleading solutions, and pathway-based analyses of large-scale genetic datasets require massive computational burden. We propose a Pathway-based approach using HierArchical components of collapsed RAre variants Of High-throughput sequencing data (PHARAOH) for the analysis of rare variants by constructing a single hierarchical model that consists of collapsed gene-...
Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Lee, S., Choi, S., Kim, Y. J., Kim, B.-J., T2d-Genes Consortium, Hwang, H., Park, T. Tags: GENES Source Type: research
Characterizing leader sequences of CRISPR loci
Motivation: The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs or their possible fun...
Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Alkhnbashi, O. S., Shah, S. A., Garrett, R. A., Saunders, S. J., Costa, F., Backofen, R. Tags: GENOME Source Type: research
MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures
Motivation: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Taxonomic analysis of microbial communities, a process referred to as binning, is one of the most challenging tasks when analyzing metagenomic reads data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species and the limitations due to short read lengths and sequencing errors.
Results: MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning. The novelty of MetaProb derives from solvin...
Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Girotto, S., Pizzi, C., Comin, M. Tags: GENOME Source Type: research
Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data
Motivation: Complex interactions among alleles often drive differences in inherited properties including disease predisposition. Isolating the effects of these interactions requires phasing information that is difficult to measure or infer. Furthermore, prevalent sequencing technologies used in the essential first step of determining a haplotype limit the range of that step to the span of reads, namely hundreds of bases. With the advent of pseudo-long read technologies, observable partial haplotypes can span several orders of magnitude more. Yet, measuring whole-genome-single-individual haplotypes remains a challenge. A di...
Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Ben-Elazar, S., Chor, B., Yakhini, Z. Tags: GENOME Source Type: research
