Ongoing improvements in throughput of the next-generation sequencing technologies challenge current generation de novo sequence assemblers. Most recent assemblers are based on construction a Bruijn graph. An alternative framework growing interest is assembly string graph, not necessitating division reads into k-mers, but requiring fast algorithms for computation suffix-prefix matches among all pairs reads. Here we present efficient methods graph from set Our approach employs suffix sorting...

The RNA-binding protein TDP-43 is heavily implicated in neurodegenerative disease. Numerous patient mutations TARDBP, the gene encoding TDP-43, combined with data from animal and cell-based models, imply that altered RNA regulation by causes Amyotrophic Lateral Sclerosis Frontotemporal Dementia. However, underlying mechanisms remain unresolved. Increased cytoplasmic levels diseased neurons suggest a possible role this cellular compartment. Here, we examined impact on translation of...

To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing ecosystem irreversibly, we sampled SMS analogous habitats Kairei and Pelagia fields along Indian Ridge. In total 19.8 million 16S rRNA tags 14 different sites were analyzed microbial communities compared with each other publicly available data sets marine environments. The chimneys appear to provide microorganisms are not found or only detectable in very low numbers...

We present data on the co-registered geochemistry (in situ mass spectrometry) and microbiology (pyrosequencing of 16S rRNA genes; V1, V2, V3 regions) in five fluid samples from Irina II Logatchev hydrothermal field. Two were collected over 24 min same spot further three spatially distinct locations (20 cm, 3 m overlaying plume). Four low-temperature fluids are composed core bacterial community, namely specific Gammaproteobacteria Epsilonproteobacteria, which, however, differs relative...

The graphical fragment assembly (GFA) formats are emerging standard for the representation of sequence graphs. Although GFA 1 was primarily targeting graphs, newer 2 format introduces several features, which makes it suitable representing other kinds information, such as scaffolding variation alignment graphs and colored metagenomic Here, we present GfaViz, an interactive tool visualization in format. software supports all new features conventions their visualization. user can choose between...

ABSTRACT The active venting Sisters Peak (SP) chimney on the Mid-Atlantic Ridge holds current temperature record for hottest ever measured hydrothermal fluids (400°C, accompanied by sudden bursts reaching 464°C). Given unprecedented regime, we investigated biome of this with a focus special microbial adaptations thermal tolerance. SP metagenome reveals considerable differences in taxonomic composition from those other vent and subsurface samples; these could be better explained than...

Microbial metabolisms in sediments play a pivotal role marine element cycling. In hydrothermal chemosynthetic microorganisms likely prevail, while non-hydrothermally impacted sediment regimes associated with organic matter decomposition are primarily recognized. To test how these distributed along the hitherto neglected transition zone influenced to different degrees by input we sampled four sites: were (i) near an active vent, (ii) outer rim, and (iii) inactive area of Kairei field as well...

The microbial community composition and its functionality was assessed for hydrothermal fluids volcanic ash sediments from Haungaroa the Brothers volcano in Kermadec island arc (New Zealand). were dominated by epsilonproteobacterial Sulfurovum sp.. Ratios of electron donor consumption to CO2 fixation respective sediment incubations indicated that sulfide oxidation appeared fuel autotrophic fixation, coinciding with thermodynamic estimates predicting as major energy source environment....

Abstract Background Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on first sequenced H. strain (XCL-2) suggested that conversion may also play role in this organism. Yet, numerous experiments underlined XCL-2’s inability to consume under tested conditions. A...

GFA 1 and 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The adopted by several software tools. Here, we present GfaPy, a package creating, parsing editing graphs using the programming language Python. GfaPy supports 2, same interface allows interconversion between both formats. provides simple custom record types, which is an important new feature of (compared to 1). This enables applications format.GfaPy available open...

The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, implementation proposed GFA specification in Ruby. It allows user to conveniently parse, edit write files. Complex operations such as separation implicit instances repeats merging linear paths performed. A typical application RGFA editing a graph, finish sequence, using...

The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, implementation proposed GFA specification in Ruby. It allows to conveniently parse, edit write files. Complex operations such as separation implicit instances repeats merging linear paths performed. A typical application RGFA editing a graph, finish sequence, using information...

Text formats are common in bioinformatics, as they allow for editing and filtering using standard tools, well as, since text often human readable, manual inspection evaluation of the data. Bioinformatics is a rapidly evolving field, hence, new techniques, software kinds data require definition formats. Often not formally described or specification document. Although libraries available accessing most formats, writing parsers which no library currently available, very though tedious task,...

The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, implementation proposed GFA specification in Ruby. It allows to conveniently parse, edit write files. Complex operations such as separation implicit instances repeats merging linear paths performed. A typical application RGFA editing a graph, finish sequence, using information...

TextFormats is a software system for efficient and user-friendly creation of text format specifications, accessible from multiple programming languages (C/C++, Python, Nim) the Unix command line. To work with format, specification written in Specification Language (TFSL) must be created. The defines datatypes each part format. syntax datatype definitions specifications based on representation. Thus this well suited description existing formats. However, when creating new representing data,...

In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy cheap. Thus it becomes feasible interesting to perform comparative genomics analyses new those related organisms. Thereby organisms can be defined by different criteria, such as taxonomy or phenotype. Expectations regarding contents are often expressed in scientific articles describing group Evaluating expectations, when a genome available, requires analysing text snippets which...

The number of available genomes prokaryotic organisms is rapidly growing enabling comparative genomics studies. comparison with a common phenotype, habitat or phylogeny often shows that these share some contents. Collecting rules expressing genome traits depending on given factors useful, as such could be used for quality control identifying interesting exceptions and formulating hypothesis. Automatizing the verification using computation tools requires definition representation schema. In...

Shaped by natural selection and other evolutionary forces, an organism's history is reflected through its genome sequence, content of functional elements organization. Consequently, organisms connected phylogeny, metabolic or morphological traits, geographical proximity, habitat features are likely to exhibit similarities in their genomes. These give rise expectations about the genomes within these organism groups. Such often informally expressed scientific literature, focusing on analysis...

Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, led an escalating accumulation of available genome data. In response this ever-expanding repository information, we introduce ProSt, a computational system designed for the batch computation, storage, and interactive visualization values attributes prokaryotic genomes. The allows parallel attribute value dynamically incrementally integrate new as...