Prediction of Effector Proteins from Trichoderma longibrachiatum Through Transcriptome Sequencing.

Trichoderma longibrachiatum SMF2 is an important biocontrol strain isolated by our group that can promote plant growth and induce plant disease resistance. To further study its biocontrol mechanism, the effector proteins secreted by T. longibrachiatum SMF2 were analyzed through bioinformatics and transcriptome sequencing. Overall, 478 secretory proteins produced by T. longibrachiatum were identified, of which 272 were upregulated after treatment with plants. Functional annotation showed that 36 secretory proteins were homologous with different groups of effectors from pathogenic microorganisms. Moreover, the quantitative PCR results of six putative effector proteins were consistent with those of transcriptome sequencing. Taken together, these findings indicate that the secretory proteins secreted by T. longibrachiatum SMF2 may act as effectors to facilitate its own growth and colonization or to induce plant immunity response.

Association of toll-like receptors polymorphisms with COPD risk in Chinese population.

Background: Previous studies have reported that the Toll-like receptors (TLRs) are related with the progress of chronic obstructive pulmonary disease (COPD). We aimed to explore the association of TLRs single nucleotide polymorphisms (SNPs) and COPD risk. Methods: 170 COPD patients and 181 healthy controls were enrolled in this case-control study. MassARRAY platform was used for genotyping seven tagging SNPs (TLR2: rs3804100, rs4696480, rs3804099; TLR3: rs3775290, rs3775291, rs5743305; TLR9: rs352140) of TLRs. The correlations between the SNPs and COPD risk were determined using logistic regression. Results: We found that the rs3775291 of TLR3 significant decreased the risk of COPD (TT versus CC: non-adjusted OR = 0.329, 95% CI = 0.123-0.879, p = 0.027). In the genetic models analysis, the rs3775291 was associated with a decreased effect of COPD based on the recessive model (TT versus CC/CT: non-adjusted OR = 0.377, 95% CI = 0.144-0.988 p = 0.047). The rs4696480 of TLR2 gene was associated with a decreased risk of COPD after adjustment by age and gender (TA versus AA: adjusted OR = 0.606, 95% CI = 0.376-0.975, p = 0.039). Conclusion: Our study showed that genetic variants in TLRs were associated with risk of COPD. The rs3775291 and rs4696480 may act as a potential biomarker for predicting the risk of COPD in Chinese population.

How Do Human-Driven Vehicles Avoid Pedestrians in Interactive Environments? A Naturalistic Driving Study.

One of the major challenges for autonomous vehicles (AVs) is how to drive in shared pedestrian environments. AVs cannot make their decisions and behaviour human-like or natural when they encounter pedestrians with different crossing intentions. The main reasons for this are the lack of natural driving data and the unclear rationale of the human-driven vehicle and pedestrian interaction. This paper aims to understand the underlying behaviour mechanisms using data of pedestrian-vehicle interactions from a naturalistic driving study (NDS). A naturalistic driving test platform was established to collect motion data of human-driven vehicles and pedestrians. A manual pedestrian intention judgment system was first developed to judge the pedestrian crossing intention at every moment in the interaction process. A total of 98 single pedestrian crossing events of interest were screened from 1274 pedestrian-vehicle interaction events under naturalistic driving conditions. Several performance metrics with quantitative data, including TTC, subjective judgment on pedestrian crossing intention (SJPCI), pedestrian position and crossing direction, and vehicle speed and deceleration were analyzed and applied to evaluate human-driven vehicles' yielding behaviour towards pedestrians. The results show how vehicles avoid pedestrians in different interaction scenarios, which are classified based on vehicle deceleration. The behaviour and intention results are needed by future AVs, to enable AVs to avoid pedestrians more naturally, safely, and smoothly.

Non-Fragile Observer-Based Adaptive Integral Sliding Mode Control for a Class of T-S Fuzzy Descriptor Systems With Unmeasurable Premise Variables.

The issue of non-fragile observer-based adaptive integral sliding mode control for a class of Takagi-Sugeno (T-S) fuzzy descriptor systems with uncertainties and unmeasurable premise variables is investigated. General nonlinear systems are represented by nonlinear T-S fuzzy descriptor models, because premise variables depend on unmeasurable system states and fuzzy models have different derivative matrices. By introducing the system state derivative as an auxiliary state vector, original fuzzy descriptor systems are transformed into augmented systems for which system properties remain the same. First, a novel integral sliding surface, which includes estimated states of the sliding mode observer and controller gain matrices, is designed to obtain estimation error dynamics and sliding mode dynamics. Then, some sufficient linear matrix inequality (LMI) conditions for designing the observer and the controller gains are derived using the appropriate fuzzy Lyapunov functions and Lyapunov theory. This approach yields asymptotically stable sliding mode dynamics. Corresponding auxiliary variables are introduced, and the Finsler's lemma is employed to eliminate coupling of controller gain matrices, observer gain matrices, Lyapunov function matrices, and/or observer gain perturbations. An observer-based integral sliding mode control strategy is obtained to assure that reachability conditions are satisfied. Moreover, a non-fragile observer and a non-fragile adaptive controller are developed to compensate for system uncertainties and perturbations in both the observer and the controller. Finally, example results are presented to illustrate the effectiveness and merits of the proposed method.

The Design, Simulation and Fabrication of an Omnidirectional Inertial Switch with Rectangular Suspension Spring.

An omnidirectional inertial switch with rectangular spring is proposed in this paper, and the prototype has been fabricated by surface micromachining technology. To evaluate the threshold consistency and stability of omnidirectional inertia switch, the stiffness of rectangular suspension springs is analyzed. The simulation result shows that the coupling stiffness of the rectangular spring suspension system in the non-sensitive direction is a little more than that in the sensitive direction, which indicated that the omnidirectional switching system's stability is reinforced, attributed to the design of rectangular springs. The dynamic response simulation shows that the threshold of the omnidirectional inertial switch using the rectangular suspension spring has high consistency in the horizontal direction. The prototype of an inertial switch is fabricated and tested successfully. The testing results indicate even threshold distribution in the horizontal direction. The threshold acceleration of the designed inertial switch is about 58 g in the X direction and 37 g in the Z direction; the contact time is about 18 µs.

Identification and Validation of Autophagy-Related Genes in Chronic Obstructive Pulmonary Disease.

PURPOSE: Autophagy plays essential roles in the development of COPD. We aim to identify and validate the potential autophagy-related genes of COPD through bioinformatics analysis and experiment validation. METHODS: The mRNA expression profile dataset GSE38974 was obtained from GEO database. The potential differentially expressed autophagy-related genes of COPD were screened by R software. Then, protein-protein interactions (PPI), correlation analysis, gene-ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied for the differentially expressed autophagy-related genes. Finally, RNA expression of top five differentially expressed autophagy-related genes was validated in blood samples from COPD patients and healthy controls by qRT-PCR. RESULTS: A total of 40 differentially expressed autophagy-related genes (14 up-regulated genes and 26 down-regulated genes) were identified between 23 COPD patients and 9 healthy controls. The PPI results demonstrated that these autophagy-related genes interacted with each other. The GO and KEGG enrichment analysis of differentially expressed autophagy-related genes indicated several enriched terms related to autophagy and mitophagy. The results of qRT-PCR showed that the expression levels of HIF1A, CDKN1A, BAG3, ERBB2 and ATG16L1 in COPD patients and healthy controls were consistent with the bioinformatics analysis results from mRNA microarray. CONCLUSION: We identified 40 potential autophagy-related genes of COPD through bioinformatics analysis. HIF1A, CDKN1A, BAG3, ERBB2 and ATG16L1 may affect the development of COPD by regulating autophagy. These results may expand our understanding of COPD and might be useful in the treatment of COPD.

Downregulation of m6 A reader YTHDC2 promotes tumor progression and predicts poor prognosis in non-small cell lung cancer.

BACKGROUND: m6 A modification affects the pathological progress of many diseases by affecting RNA stability and translocation. YTHDC2, a m6 A reader, is associated with multiple cancers; however, little is known of its role in non-small cell lung cancer (NSCLC). METHODS: The GEPIA, Oncomine and GEO databases were analyzed to assess expression of YTHDC2 in NSCLC patients. Quantitative polymerase chain reaction, western blot and immunohistochemistry were used to detect YTHDC2 expression in different NSCLC cell lines (H1299, H460, H292 and A549) and patients. The effects of YTHDC2 on NSCLC cell lines (A549 and H1299) proliferation and migration were employed using CCK8 and transwell assays. The potential target RNAs of YTHDC2 were obtained from the POSTAR database. Functional enrichment analysis of YTHDC2 targeted RNAs was performed using the Metascape database. RESULTS: GEPIA, Oncomine and GEO databases showed low expression of YTHDC2 in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. YTHDC2 expression was significantly decreased in different NSCLC cell lines and our clinical samples. Moreover, low expression of YTHDC2 was significantly associated with poor differentiation, lymph node metastasis, tumor size and stage. In addition, YTHDC2 could suppress the proliferation and migration ability of A549 and H1299 cell lines. Kaplan-Meier Plotter database analysis revealed that patients with low level of YTHDC2 had a significantly poor prognosis. Finally, functional enrichment analysis of YTHDC2 targeted RNAs indicated several enriched pathways related to cancer. CONCLUSIONS: These findings elucidate that YTHDC2 suppresses tumorigenesis in NSCLC, indicating that YTHDC2 may be a promising therapeutic target for NSCLC. KEY POINTS: SIGNIFICANT FINDINGS OF THE STUDY: This study demonstrated that the downregulation of YTHDC2 promotes tumor progression and predicts poor prognosis in non-small cell lung cancer (NSCLC). WHAT THIS STUDY ADDS: YTHDC2 might be a promising therapeutic target for non-small cell lung cancer (NSCLC).

Metatranscriptomic identification of polyamine-transforming bacterioplankton in the Gulf of Mexico.

The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.

Comparison of commonly used solid tumor targeted gene sequencing panels for estimating tumor mutation burden shows analytical and prognostic concordance within the cancer genome atlas cohort.

BACKGROUND: Tumor mutation burden (TMB) is a biomarker frequently reported by clinical laboratories, which is derived by quantifying of the number of single nucleotide or indel variants (mutations) identified by next-generation sequencing of tumors. TMB values can inform prognosis or predict the response of a patient's tumor to immune checkpoint inhibitor therapy. Methods for the calculation of TMB are not standardized between laboratories, with significant variables being the gene content of the panels sequenced and the inclusion or exclusion of synonymous variants in the calculations. The impact of these methodological differences has not been investigated and the concordance of reported TMB values between laboratories is unknown. METHODS: Sequence variant lists from more than 9000 tumors of various types were downloaded from The Cancer Genome Atlas. Variant lists were filtered to include only appropriate variant types (ie, non-synonymous only or synonymous and non-synonymous variants) within the genes found in five commonly used targeted solid tumor gene panels as well as an in-house gene panel. Calculated TMB was paired with corresponding overall survival (OS) data of each patient. RESULTS: Regression analysis indicates high concordance of TMB as derived from the examined panels. TMB derived from panels was consistently and significantly lower than that derived from a whole exome. TMB, as derived from whole exome or the examined panels, showed a significant correlation with OS in the examined data. CONCLUSIONS: TMB derived from the examined gene panels was analytically equivalent between panels, but not between panels and whole-exome sequencing. Correlation between TMB and OS is significant if TMB method-specific cut-offs are used. These results suggest that TMB values, as derived from the gene panels examined, are analytically and prognostically equivalent.

The Analysis of the Influence of Threshold on the Dynamic Contact Process of a Fabricated Vertically Driven MEMS Inertial Switch.

In this work, to evaluate the influence of the threshold on the dynamic contact process, five models (number 1, 2, 3, 4, 5) with different thresholds were proposed and fabricated with surface micromachining technology. The contact time and response time were used to characterize the dynamic contact performance. The dynamic contact processes of the inertial switches with gradually increasing thresholds were researched using analytical, simulation, and experimental methods. The basic working principle analysis of the inertial switch shows that the contact time of the inertial switch with a low-g value can be extended by using a simply supported beam as the fixed electrode, but the high-G inertial needs more elasticity for fixed electrode. The simulation results indicate that the response time and contact time decrease with the increment in the designed threshold. Prototypes were tested using a dropping hammer system, and the test result indicates that the contact time of the inertial switch with a fixed electrode of the simply supported beam is about 15 and 5 µs when the threshold is about 280 and 580 g, respectively. Meanwhile, the contact time can be extended to 100 µs for the inertial switch using a spring as the fixed electrode when the threshold is about 280 and 580 g. These test results not only prove that the spring fixed electrode can effectively extend the contact time, but also prove that the style of the fixed electrode is the deciding factor affecting the contact time of the high-G inertial switch.

Bioinformatics Basics for High-Throughput Hybridization-Based Targeted DNA Sequencing from FFPE-Derived Tumor Specimens: From Reads to Variants.

The use of next-generation sequencing and hybridization-based capture for target enrichment have enabled the interrogation of coding regions of several clinically significant cancer genes in tumor specimens using both targeted panels of a few to hundreds of genes, to whole-exome panels encompassing coding regions of all genes in the genome. Next-generation sequencing (NGS) technologies produce millions of relatively short segments of sequences or reads that require bioinformatics tools to map reads back to a reference genome using various read alignment tools, as well as to determine differences between single bases (single nucleotide variants or SNVs) or multiple bases (insertions and deletions or indels) between the aligned reads and the reference genome to call variants. In addition to single nucleotide changes or small insertions and deletions, high copy gains and losses can also be gleaned from NGS data to call gene amplifications and deletions. Throughout these processes, numerous quality control metrics can be assessed at each step to ensure that the resulting called variants are of high quality and are accurate. In this chapter we review common tools used to generate reads from Illumina-derived sequence data, align reads, and call variants from hybridization-based targeted NGS panel data generated from tumor FFPE-derived DNA specimens as well as basic quality metrics to assess for each assayed specimen.

Annotation of Variant Data from High-Throughput DNA Sequencing from Tumor Specimens: Filtering Strategies to Identify Driver Mutations.

The use of next-generation sequencing technologies has enabled the analysis of a wide spectrum of somatic mutations in tumors. This analysis can be carried out using various strategies including the use of small panels of focused, clinically actionable genes, large panels of cancer-related genes, whole exomes, and the entire genome. One of the main goals in these analyses is to identify key mutations in these tumors that drive the oncogenic process. Depending on the gene, mutations can have altering effects, such as loss of function mutations in tumor suppressor genes, to mutations that activate genes such as kinases involved with cell cycle progression or proliferation. Once the sequencing process is complete, and the alignment of the large collection of reads to the reference genome and variant calling has been carried out, one is left with a large collection of variants. The challenge then becomes assigning where the variant resides in the genome with respect to coding regions, splice site regions, regulatory regions, and what potential functional effect these variants may have on the resulting protein. Other helpful information includes determining if the variant has been identified before, and if so, the tumor type associated with the variant. In addition, if the tumor profiling experiment is not conducted with a matched specimen representing the inherited genome, various tools are helpful to determine if the variant is likely to be an inherited polymorphism or a somatic event. In this chapter, we review the various tools available for annotating variants to assist in filtering down and prioritizing the hundreds to thousands of variants down to the key variants likely to be driver mutations and relevant to the tumor being profiled.

The Elastic Contact and Stability Analysis of an Inertial Micro-Switch with a Spring Stationary Electrode.

A mechanical trigger inertial micro-switch with spring stationary electrode is proposed and fabricated by surface micromachining. The elastic contact process and stability performance are evaluated through experimental tests performed using a drop hammer. The test results show that the contact time is about 110 µs and 100 µs when the threshold acceleration is 480 g and the overload acceleration is 602 g, respectively. The vibration process of the electrodes is explained through an established physical mode. The elastic contact process is analyzed and discussed by Finite Element Analysis (FEA) simulations, which indicated that the contact time is about 65 µs when the threshold acceleration is 600 g. At the same time, this result also proved that the contact time could be extended effectively by the designed spring stationary electrode. The overload acceleration (800 g) has been applied to the Finite-Element model in ANSYS, the contact process indicated that the proof mass contacted with stationary electrode three times, and there was no bounce phenomenon during contact process, which fully proved that the stable contact process can be realized at high acceleration owing to the designed elastic stationary electrode.

Identification of polyamine-responsive bacterioplankton taxa in South Atlantic Bight.

Putrescine and spermidine are short-chained aliphatic polyamines (PAs) that are ubiquitously distributed in seawater. These compounds may be important sources of dissolved organic carbon and nitrogen for marine bacterioplankton. Here, we used pyrotag sequencing to quantify the response of bacterioplankton to putrescine and spermidine amendments in microcosms established using surface waters collected at various stations in the South Atlantic Bight in October 2011. Our analysis showed that PA-responsive bacterioplankton consisted of bacterial taxa that are typically dominant in marine systems. Rhodobacteraceae (Alphaproteobacteria) was the taxon most responsive to PA additions at the nearshore site. Gammaproteobacteria of the families Piscirickettsiaceae; Vibrionaceae; and Vibrionaceae and Pseudoalteromonadaceae, were the dominant PA-responsive taxa in samples from the river-influenced coastal station, offshore station and open ocean station, respectively. The spatial variability of PA-responsive taxa may be attributed to differences in composition of the initial bacterial community and variations of in situ physiochemical conditions among sites. Our results also provided the first empirical evidence that Gammaproteobacteria might play an important role in PA transformation in marine systems.

Temporal and vertical distributions of bacterioplankton at the Gray's Reef National Marine Sanctuary.

Large spatial scales and long-term shifts of bacterial community composition (BCC) in the open ocean can often be reliably predicted based on the dynamics of physical-chemical variables. The power of abiotic factors in shaping BCC on shorter time scales in shallow estuarine mixing zones is less clear. We examined the diurnal variation in BCC at different water depths in the spring and fall of 2011 at a station in the Gray's Reef National Marine Sanctuary (GRNMS). This site is located in the transition zone between the estuarine plume and continental shelf waters of the South Atlantic Bight. A total of 234,516 pyrotag sequences of bacterial 16S rRNA genes were recovered; they were taxonomically affiliated with >200 families of 23 bacterial phyla. Nonmetric multidimensional scaling analysis revealed significant differences in BCC between spring and fall samples, likely due to seasonality in the concentrations of dissolved organic carbon and nitrate plus nitrite. Within each diurnal sampling, BCC differed significantly by depth only in the spring and differed significantly between day and night only in the fall. The former variation largely tracked changes in light availability, while the latter was most correlated with concentrations of polyamines and chlorophyll a. Our results suggest that at the GRNMS, a coastal mixing zone, diurnal variation in BCC is attributable to the mixing of local and imported bacterioplankton rather than to bacterial growth in response to environmental changes. Our results also indicate that, like members of the Roseobacter clade, SAR11 bacteria may play an important role in processing dissolved organic material in coastal oceans.

Microspatial gene expression patterns in the Amazon River Plume.

We investigated expression of genes mediating elemental cycling at the microspatial scale in the ocean's largest river plume using, to our knowledge, the first fully quantitative inventory of genes and transcripts. The bacterial and archaeal communities associated with a phytoplankton bloom in Amazon River Plume waters at the outer continental shelf in June 2010 harbored ∼ 1.0 × 10(13) genes and 4.7 × 10(11) transcripts per liter that mapped to several thousand microbial genomes. Genomes from free-living cells were more abundant than those from particle-associated cells, and they generated more transcripts per liter for carbon fixation, heterotrophy, nitrogen and phosphorus uptake, and iron acquisition, although they had lower expression ratios (transcripts ⋅ gene(-1)) overall. Genomes from particle-associated cells contributed more transcripts for sulfur cycling, aromatic compound degradation, and the synthesis of biologically essential vitamins, with an overall twofold up-regulation of expression compared with free-living cells. Quantitatively, gene regulation differences were more important than genome abundance differences in explaining why microenvironment transcriptomes differed. Taxa contributing genomes to both free-living and particle-associated communities had up to 65% of their expressed genes regulated differently between the two, quantifying the extent of transcriptional plasticity in marine microbes in situ. In response to patchiness in carbon, nutrients, and light at the micrometer scale, Amazon Plume microbes regulated the expression of genes relevant to biogeochemical processes at the ecosystem scale.

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments.

Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.

Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data.

SUMMARY: Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are not suitable for alignment data in metagenomics, which are often interspecies alignments. We have developed a web browser-based desktop application for interactively visualizing alignment data of metagenomic sequences. This viewer is easy to use on all computer systems with modern web browsers and requires no software installation. AVAILABILITY: http://weizhongli-lab.org/mgaviewer