VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing preparing metagenomics, genomics population nucleotide sequence data. It designed as alternative to the widely used USEARCH (Edgar, 2010) which code not publicly available, algorithm details are only rudimentarily described, a memory-confined 32-bit version freely available academic use.When searching sequences, uses fast heuristic based on words shared by query target sequences in order quickly identify...

The publication of a complete genome sequence is usually accompanied by annotations its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA difficult. We have therefore created computational predictors the major species from all kingdoms life and compiled them into program called RNAmmer. uses hidden Markov models trained data 5S database European project. A pre-screening step...

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues first nearly identical amplicons iteratively using a local threshold, then clusters' internal structure abundances refine its results. This fast, scalable, independent approach reduces the influence of parameters produces robust operational taxonomic units.

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global thresholds input-order dependency. v1 worked with an initial phase used iterative single-linkage local threshold (d), followed by the internal abundance structures clusters to break chained OTUs. Here present v2, which has two important features: (1) new algorithm for d = 1 allows computation time scale linearly...

Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated performance recently released state-of-the-art open-source software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST USEARCH) QIIME, hierarchical methods mothur, USEARCH's most recent algorithm,...

Abstract Motivation: Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm that Smith–Waterman. However, because computationally demanding nature this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has obtained at cost reduced sensitivity very expensive hardware. Results: A fast implementation Smith–Waterman sequence-alignment using...

The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods database searching, but also time-consuming. fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. aim of this study was explore whether further speed could be gained other approaches parallelisation. A faster and implementation benchmarked. In the new tool SWIPE, residues from sixteen different sequences are compared parallel one query...

AlkB homolog 1 (ALKBH1) is one of nine members the family mammalian homologs. Most Alkbh1(-/-) mice die during embryonic development, and survivors are characterized by defects in tissues originating from ectodermal lineage. In this study, we show that deletion Alkbh1 prolonged expression pluripotency markers stem cells delayed induction genes involved early differentiation. vitro differentiation to neural progenitor (NPCs) displayed an increased rate apoptosis NPCs when compared with...

Abstract Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) are free of arbitrary global thresholds. Here, present swarm v3 to address issues contemporary datasets growing towards tera-byte sizes. Results When compared with previous versions, has modernized C++ source code, reduced memory footprint by up 50%, optimized CPU-usage and multithreading (more than 7 times faster default...

Abstract Motivation The AOP-Wiki, a knowledge database for Adverse Outcome Pathways (AOPs), requires an efficient way to present overview of its content the reconstruction networks by experts in given domain. We have developed AOP-networkFinder, user-friendly tool that retrieves AOPs interest, allows network generation and cleaning, finally visualizes built around retrieved AOPs. Our constructs AOP connecting use same Key Events (KEs) versatile but controlled manner. Genes related these KEs...

Endonuclease III from Escherichia coli is the prototype of a ubiquitous DNA repair enzyme essential for removal oxidized pyrimidine base damage. The yeast genome project has revealed presence two genes in Saccharomyces cerevisiae,NTG1 and NTG2, encoding proteins with similarity to endonuclease III. Both contain highly conserved helix-hairpin-helix motif, whereas only one (Ntg2) harbors characteristic iron-sulfur cluster family. We have characterized these gene functions by mutant analysis as...

Huntington's disease (HD) is one of several neurodegenerative disorders caused by expansion CAG repeats in a coding gene. Somatic rates HD vary between organs, and the greatest instability observed brain, correlating with neuropathology. The fundamental mechanisms somatic repeat are poorly understood, but locally formed secondary DNA structures generated during replication and/or repair believed to underlie triplet expansion. Recent studies mice have demonstrated that mismatch (MMR) base...

The functions of several SOS regulated genes in Escherichia coli are still unknown, including dinQ. In this work we characterize dinQ and two small RNAs, agrA agrB, with antisense complementarity to Northern analysis revealed five transcripts, but only one transcript (+44) is actively translated. +44 translates into a toxic single transmembrane peptide localized the inner membrane. AgrB regulates RNA by interference counteract DinQ toxicity. Thus dinQ-agr locus shows classical features type...

Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to reference genome, or two genomes each other. The purpose the comparison usually find where differ, e.g. subsequence repeated deleted, insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none them 1) provides detailed information about types and locations all differences between...

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It designed as alternative to the widely used USEARCH (Edgar 2010) which code not publicly available, algorithm details are only rudimentarily described, a memory-confined 32-bit version freely available academic use. Methods. When searching sequences, uses fast heuristic based on words shared by query target sequences in order quickly identify similar...

Abstract The oxidation resistance gene 1 ( OXR1 ) is crucial for protecting against oxidative stress; however, its molecular function unknown. We employed RNA sequencing to examine the role of human genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, depletion resulted down-regulation 554 genes up-regulation 253 genes. These differentially expressed include factors (i.e. HIF1A , SP6, E2F8 TCF3 ), antioxidant PRDX4 PTGS1 CYGB numerous p53...

Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated uracil-DNA glycosylase (UNG) or single-strand selective monofunctional (SMUG1). The relative in vivo contributions of each remain elusive. To assess the impact SMUG1 deficiency, we measured 5-hydroxymethyluracil, another substrate, Smug1 -/- mice. We found that 5-hydroxymethyluracil accumulated tissues correlated with 5-hydroxymethylcytosine levels....

As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and granuloma. Understanding Mtb responses to stress essential identify new virulence factors pathways that play a role in survival of tubercle bacillus. The main goal this study was map regulatory networks differentially expressed (DE) transcripts upon various forms genotoxic stress. We exposed cells oxidative (H2O2 or paraquat), nitrosative (DETA/NO), alkylation...

Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT from 1034 CRCbiome participants, recruited a Norwegian study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent them assigned to known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles comprehensive lifestyle...

Background: Bacteriophages (phages) are recognized as key regulators of microbial communities, and it is pivotal to understand viral ecology, diversity, evolution. However, identification characterization phages from shotgun metagenome sequencing pose unique bioinformatic challenges owing the inherent complexity scale data. Results: Here, we introduce VirMake, a comprehensive, flexible, scalable pipeline developed for taxonomic functional analysis It enables high-throughput end-to-end...

Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat sequences in the human pathogens Neisseriameningitidis, Neisseria gonorrhoeae and Haemophilus influenzae found that by far most frequent 9–10mers residing within coding regions DNA uptake (DUS) required natural genetic transformation. More importantly, we significantly higher density DUS genes involved repair, recombination, restriction‐modification replication than any...