Tool For Comparative Analysis Research Articles

Real time visualization and characterization of platelet deposition under flow onto clinically relevant opaque surfaces

Although the thrombogenic nature of the surfaces of cardiovascular devices is an important aspect of blood biocompatibility, few studies have examined platelet deposition onto opaque materials used for these devices in real time. This is particularly true for the metallic surfaces used in current ventricular assist devices (VADs). Using hemoglobin depleted red blood cells (RBC ghosts) and long working distance optics to visualize platelet deposition, we sought to perform such an evaluation. Fluorescently labeled platelets mixed with human RBC ghosts were perfused across six opaque materials (a titanium alloy (Ti6Al4V), silicon carbide (SiC), alumina (Al2O3, 2-methacryloyloxyethyl phosphorylcholine polymer coated Ti6Al4V (MPC-Ti6Al4V), yttria partially stabilized zirconia (YZTP), and zirconia toughened alumina (ZTA)) for 5 min at wall shear rates of 400 and 1000 s(-1). Ti6Al4V had significantly increased platelet deposition relative to MPC-Ti6Al4V, Al2 O3 , YZTP, and ZTA at both wall shear rates (p < 0.01). For all test surfaces, increasing the wall shear rate produced a trend of decreased platelet adhesion. The described system can be a utilized as a tool for comparative analysis of candidate blood-contacting materials with acute blood contact.

Simultaneous Alignment and Folding of Protein Sequences

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise and multiple sequence alignment tools in the most difficult low-sequence homology case. It also improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families (partiFold-Align is available at http://partifold.csail.mit.edu/ ).

StaphyloBase: a specialized genomic resource for the staphylococcal research community

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

BackgroundDivergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes.ResultsWe inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to ~80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases.ConclusionsWe have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http://complex.plantgenie.org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e.g. finding candidate genes for perturbation experiments.

Design, synthesis, pharmacological evaluation and in silico ADMET prediction of novel substituted benzimidazole derivatives as angiotensin II–AT1 receptor antagonists based on predictive 3D QSAR models

In this study we designed novel substituted benzimidazole derivatives and predicted their absorption, distribution, metabolism, excretion and toxicity (ADMET) properties, based on a predictive 3D QSAR study on 132 substituted benzimidazoles as AngII–AT1 receptor antagonists. The two best predicted compounds were synthesized and evaluated for AngII–AT1 receptor antagonism. Three different alignment tools for comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used. The best 3D QSAR models were obtained using the rigid body (Distill) alignment method. CoMFA and CoMSIA models were found to be statistically significant with leave-one-out correlation coefficients (q2) of 0.630 and 0.623, respectively, cross-validated coefficients (r2cv) of 0.651 and 0.630, respectively, and conventional coefficients of determination (r2) of 0.848 and 0.843, respectively. 3D QSAR models were validated using a test set of 24 compounds, giving satisfactory predicted results (r2pred) of 0.727 and 0.689 for the CoMFA and CoMSIA models, respectively. We have identified some key features in substituted benzimidazole derivatives, such as lipophilicity and H-bonding at the 2- and 5-positions of the benzimidazole nucleus, respectively, for AT1 receptor antagonistic activity. We designed 20 novel substituted benzimidazole derivatives and predicted their activity. In silico ADMET properties were also predicted for these designed molecules. Finally, the compounds with best predicted activity were synthesized and evaluated for in vitro angiotensin II–AT1 receptor antagonism.

CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.

HelicoBase: a Helicobacter genomic resource and analysis platform.

BackgroundHelicobacter is a genus of Gram-negative bacteria, possessing a characteristic helical shape that has been associated with a wide spectrum of human diseases. Although much research has been done on Helicobacter and many genomes have been sequenced, currently there is no specialized Helicobacter genomic resource and analysis platform to facilitate analysis of these genomes. With the increasing number of Helicobacter genomes being sequenced, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of diseases caused by Helicobacter pathogens.DescriptionTo facilitate the ongoing research on Helicobacter, a specialized central repository and analysis platform for the Helicobacter research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data, particularly comparative analysis. Here we present HelicoBase, a user-friendly Helicobacter resource platform with diverse functionality for the analysis of Helicobacter genomic data for the Helicobacter research communities. HelicoBase hosts a total of 13 species and 166 genome sequences of Helicobacter spp. Genome annotations such as gene/protein sequences, protein function and sub-cellular localisation are also included. Our web implementation supports diverse query types and seamless searching of annotations using an AJAX-based real-time searching system. JBrowse is also incorporated to allow rapid and seamless browsing of Helicobacter genomes and annotations. Advanced bioinformatics analysis tools consisting of standard BLAST for similarity search, VFDB BLAST for sequence similarity search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis are also included to facilitate the analysis of Helicobacter genomic data.ConclusionsHelicoBase offers access to a range of genomic resources as well as tools for the analysis of Helicobacter genome data. HelicoBase can be accessed at http://helicobacter.um.edu.my.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-600) contains supplementary material, which is available to authorized users.

Benchmarking the Higher Education Institutions in Egypt using Composite Index Model

Egypt has the largest and most significant higher education system in the Middle East and North Africa but it had been continuously facing serious and accumulated challenges. The Higher Education Institutions in Egypt are undergoing important changes involving the development of performance, they are implementing strategies to enhance the overall performance of their universities using ICT, but still the gap between what is existing and what is supposed to be for the self-regulation and improvement processes is not entirely clear to face these challenges. The using of strategic comparative analysis model and tools to evaluate the current and future states will affect the overall performance of universities and shape new paradigms in development of Higher Education System (HES), several studies have investigated the evaluation of universities through the development and use of ranking and benchmark systems In this paper, we provide a model to construct unified Composite Index (CI) based on a set of SMART indictors emulate the nature of higher education systems in Egypt. The outcomes of the proposed model aim to measure overall performance of universities and provide unified benchmarking method in this context. The model was discussed from theoretical and technical perspectives. Meanwhile, the research study was conducted with 40 professors from 19 renowned universities in Egypt as education domain experts.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.

Using the rural web in dialogue with regional stakeholders

Globalization transforms rural places through different ways, resulting in a newly differentiated countryside. Some regions appear to be more successful than others in reacting to the opportunities and threats that accompany these globalization processes. These change processes also resulted in the need for new theoretical frameworks, tackling the nature, dynamics and heterogeneity of rural development processes. The rural web (van der Ploeg and Marsden, 2008) is one of these new comprehensive theoretical frameworks on rural development. The web not only offers a tool for comparative analysis of different development paths both within and between regions, it can also be used as a diagnostic tool for exploring the potentials and limits of rural development patterns.It is within this context of a changing and globalizing countryside that the Social Sciences Unit of ILVO was approached by the coordinators of two LEADER-areas in Flanders. They wanted to take the bottom-up philosophy of LEADER a step further and wanted to involve local actors in writing the Local Development Strategy (LDS). The LEADER-coordinators were however faced with a lack of engagement techniques and tools to facilitate the dialogue with the local community. Therefore we explored the possibilities of using the rural web, not only as an analytical tool, but also as a mobilizing tool that can actively engage actors in reflecting on the development of their region. Based on a case-study research in two regions in Flanders we believe that we succeeded in adding an innovative applicability of the web. If certain preconditions are met, it lives up to the expectation of enriching the dialogue with regional actors. Furthermore, it can enable local actors to assess the state of their own region and to position it within a broader picture of changing rural areas.

Metadata-driven comparative analysis tool for sequences (meta-CATS): An automated process for identifying significant sequence variations that correlate with virus attributes

The Virus Pathogen Resource (ViPR; www.viprbrc.org) and Influenza Research Database (IRD; www.fludb.org) have developed a metadata-driven Comparative Analysis Tool for Sequences (meta-CATS), which performs statistical comparative analyses of nucleotide and amino acid sequence data to identify correlations between sequence variations and virus attributes (metadata). Meta-CATS guides users through: selecting a set of nucleotide or protein sequences; dividing them into multiple groups based on any associated metadata attribute (e.g. isolation location, host species); performing a statistical test at each aligned position; and identifying all residues that significantly differ between the groups. As proofs of concept, we have used meta-CATS to identify sequence biomarkers associated with dengue viruses isolated from different hemispheres, and to identify variations in the NS1 protein that are unique to each of the 4 dengue serotypes. Meta-CATS is made freely available to virology researchers to identify genotype-phenotype correlations for development of improved vaccines, diagnostics, and therapeutics.

Contemplating Chinese Foreign Policy: Approaches to the Use of Historical Analysis

Many have contemplated Chinese foreign policy and its future direction, but few have queried how Chinese history might illuminate both. This is unfortunate since researchers have shown that history can influence foreign policy agendas, discourses, and national goals. Moreover, it provides an invaluable tool for comparative analysis. The purpose of this introduction is to provide historical background to the articles comprising this special issue, whose contributors employ historical analysis, with the period preceding and following the Xinhai Revolution as a basis, to illuminate contemporary Chinese foreign policy – e.g., China's interest in remaking the international order and its security norms – or to suggest differences between past and present – for example, in regards to China's Asia–Pacific posture. This introduction also hopes to stimulate further work on Chinese history and foreign policy by highlighting similarities and differences between past and present with respect to, inter alia, pressures against China's territorial integrity, sovereignty, and independence, the penetration of foreign actors and ideas into China, and domestic factors limiting China's efforts to filter external influences and to respond to them.

A Comparative Analysis of How Actors Implement: Testing the Contextual Interaction Theory in 48 Cases of Wetland Restoration

This paper applies a two-actor, causal, deductive theory of implementation (the contextual interaction theory) to analyze 48 wetland restoration cases. The theory uses motivation, information, and power of the policy implementer and target to predict the nature of the implementation process (e.g. cooperation, obstruction, etc.). The research question centers on the predictability potential of the contextual interaction theory. It asks if the theory accurately predicts process interactions, based on the quantification of actor motivation, information, and power. In the analysis, a strong correlation was found between expected and observed results, or a high predictability potential. To overcome limitations, a formula version was also tested using a correlation design. These results did not produce an equivalent fit. One explanation is that implementation entails threshold values in the core variables, and a broad neutral category that fails to influence action in the same manner. This theory is found to be a useful tool for consistent, comparative, and replicable analyses that should be applied more broadly in implementation studies to better understand its strengths and limitations.

The burden of mental disorders in the USA: new tools for comparative analysis of health outcomes between countries

BackgroundThe global burden of mental disorders and substance abuse has increased 38% in absolute terms (5·8% per capita) between 1990 and 2010, from 5·3% to 7·4% of total disability-adjusted life-years (DALYs). Given the increasing importance of mental disorders worldwide, particularly for young adults, how can we make meaningful comparisons to determine which countries' policies have been effective in reducing their burden? This research will demonstrate new methods for comparative analysis highlighting the burden of mental disorders in the USA. MethodsMental burden estimates were derived as part of the Global Burden of Disease Study (GBD) 2010. To make meaningful comparisons across time, age-standardised DALY rates were utilised to adjust for changes in population size and age structure. FindingsAge-standardised DALY rates for mental disorders in the USA increased 13% between 1990 and 2010, from 3162 to 3576 DALYs per 100 000; by contrast, all developed countries increased 5% from 3016 to 3169. This increase in the USA was primarily due to substance abuse (65%) and major depression (13%). Across the 187 countries analysed, with highest rank indicating worst burden, the USA ranked 162nd for mental disorders in 2010. For specific conditions, ordered from highest to lowest burden, the USA ranked 56th for major depression (945 per 100 000), 183rd for drug use (743), 164th for anxiety (594), 138th for alcohol use (354), 179th for schizophrenia (242), and 52nd for bipolar disorder (186). Taking uncertainty into account, drug abuse was the only condition for which the USA performed significantly worse (p<0·0001) compared with the global mean. InterpretationThe USA consistently ranks below other developed nations and many developing nations for mental disorders despite spending 17·6% (US$2·5 trillion) of its gross domestic product on health in 2010, with 5% of that on mental health, among the highest of any country. This makes a compelling case for re-examination of how the USA should reprioritise mental health policy and funding. For substance abuse, countries that emphasise harm reduction policies (Netherlands, Belgium, Germany) perform substantially better than do those focused on penalisation (USA, UK, Italy, Spain). For anxiety and depression, prescription of psychotropic drugs in lieu of the more effective types of psychotherapy may have led to little improvement despite large expenditure. Further data collection on prevalence and severity of mental disorders is necessary to improve comparisons between countries. FundingBill & Melinda Gates Foundation.

Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis

PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to document and analyze artifacts associated with multiband signatures and preferential template amplification and to highlight their impacts on the use of this technique for quantitative diversity analysis. Six bacterial species (three Betaproteobacteria, two Alphaproteobacteria, and one Firmicutes) were amplified individually and in combinations with primers targeting the V7/V8 region of the 16S rRNA gene. Two of the six isolates produced multiband profiles demonstrating that band number does not correlate directly with α-diversity. Analysis of the multiple bands from one of these isolates confirmed that both bands had identical sequences which lead to the hypothesis that the multiband pattern resulted from two distinct structural conformations of the same amplicon. In addition, consistent preferential amplification was demonstrated following pairwise amplifications of the six isolates. DGGE and real time PCR analysis identified primer mismatch and PCR inhibition due to 16S rDNA secondary structure as the most probable causes of preferential amplification patterns. Reproducible DGGE community profiles generated in this study confirm that PCR-DGGE provides an excellent high-throughput tool for comparative community structure analysis, but that method-specific artifacts preclude its use for accurate comparative diversity analysis.

International Comparative Analysis of Building Regulations: An Analytical Tool

The aim of this paper is to introduce a tool for the international comparative analysis of regulatory regimes in the field of building regulation. On the basis of a heuristic model drawn from regulatory literature, a typology of building regulatory regimes is introduced. Each type is illustrated with a number of real-life examples from North America, Europe and Australia. The comparative analysis of different regimes assists policy makers by demonstrating which combinations of regulatory characteristics can provide the best results in particular instances. The typology introduced by the paper assists this process by providing a tool for systematic analysis of complex real-life cases.

Temi e problemi del cristianesimo antico in prospettiva storico-religiosa : Ugo Bianchi e il metodo comparativo

The fundamental requirement of Ugo Bianchi’s scientific pursuit was to combine two basic guiding principles in a single frame of reference : idiographic research concerned with the ‘particular’ in its irreducible historic specificity, and the construction of a vast comparative structure suitable for showing similarities and differences between diverse phenomena and between their respective processes of formation and development. Over the long course of the scholar’s scientific journey, Christian religious tradition constituted an important subject of investigation to which the tools of comparative and idiographic analysis were always applied with expertise and adaptability in a project intended to legitimately include, as historical religious subject matter, Christian issues usually deemed to be the specific, if not exclusive, province of disciplines such as the history of Christianity, Christian literature, biblical exegesis, and theology.

Using Compliance Analysis for PPP to bridge the gap between SEA and EIA: Lessons from the Turcot Interchange reconstruction in Montréal, Québec

There is increasing concern about the disjunct between the intent of higher level government goals and actual projects “on the ground” in Canada. Although strategic environmental assessment (SEA) and a wide variety of plans, policies and programmes (PPP) contain and promote goals that envision a movement towards social, economic and environmental sustainability, these goals are not necessarily upheld by large-scale projects and their environmental impact assessments (EIAs). This disconnect is often illustrated through anecdotal observations. However, to be able to overcome this disjunct it is imperative to come to a clearer understanding of the degree of sustainability or unsustainability of large-scale developments and the way in which they “measure up” in terms of the goals when compared to alternative options.This article proposes a Compliance Analysis method for investigating the level of harmonization between SEA, PPP and proposed projects and their possible alternatives (CAPPP). This method is quantified through a Likert scale which allows for comparison of alternatives for decision making and analytical purposes. The 2009 proposal for the Turcot Exchange redevelopment in Montréal, Québec, put forward by the Ministry of Transport of Québec (MTQ), as well as two alternative proposals, were utilized as a case study to clearly demonstrate the CAPPP methodology and its applicability.The approved plan for the Turcot redevelopment proposed by MTQ was found to be in poor compliance with the majority of the 178 goals in the six sectors that were examined (air quality, climate change, health, noise, socioeconomic, transport), while alternative proposals were found to be in greater accordance with the intentions of governmental SEA and PPP.Synthesis and applications: The CAPPP methodology is a versatile “watchdog” tool for the examination of the level of compliance between stated goals for regions, industrial sectors, or governments and the EIAs of concrete projects “on the ground”. CAPPP can be used as a tool for comparative analysis in decision-making situations at various scales. CAPPP is a fairly straight-forward method that can be used by policy makers, EIA experts, and members of the general public alike.

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.

MetaSAMS—A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

Metagenomics aims at exploring microbial communities concerning their composition and functioning. Application of high-throughput sequencing technologies for the analysis of environmental DNA-preparations can generate large sets of metagenome sequence data which have to be analyzed by means of bioinformatics tools to unveil the taxonomic composition of the analyzed community as well as the repertoire of genes and gene functions. A bioinformatics software platform is required that allows the automated taxonomic and functional analysis and interpretation of metagenome datasets without manual effort. To address current demands in metagenome data analyses, the novel platform MetaSAMS was developed. MetaSAMS automatically accomplishes the tasks necessary for analyzing the composition and functional repertoire of a given microbial community from metagenome sequence data by implementing two software pipelines: (i) the first pipeline consists of three different classifiers performing the taxonomic profiling of metagenome sequences and (ii) the second functional pipeline accomplishes region predictions on assembled contigs and assigns functional information to predicted coding sequences. Moreover, MetaSAMS provides tools for statistical and comparative analyses based on the taxonomic and functional annotations. The capabilities of MetaSAMS are demonstrated for two metagenome datasets obtained from a biogas-producing microbial community of a production-scale biogas plant. The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de.