Alignment Gaps Research Articles

Enhancing photocatalytic hydrogen evolution of g-C3N4 via oxygen-containing groups

This study investigates the impact of three oxygen-containing functional groups (–COOH, –CO, and –OH) on the photocatalytic performance of graphitic carbon nitride (g-C3N4) in the context of the hydrogen evolution reaction (HER) using first principles calculations. Our analysis of the Gibbs free energy of HER reveals that functionalized g-C3N4 in quadrant III exhibits a significantly reduced overpotential of −1.19 eV compared to pristine g-C3N4. Moreover, g-C3N4–(OHQI + OQII + COOHQIII) and g-C3N4–(OQI + OHQII + COOHQIII) demonstrate exceptional light harvesting capabilities in the 350–800 nm range, attributed to anisotropic and steric hindrance effects. Furthermore, g-C3N4–OHQIII and g-C3N4–(OHQI + COOHQIII) exhibit favorable band alignment and narrower band gaps of 2.55 and 2.39 eV, respectively, indicating suitable band edge positions for catalytic HER activities. This work offers valuable insights into the photocatalytic mechanisms and electronic properties of oxygen-containing functional groups modified g-C3N4, paving the way for new applications in solar water splitting with tailored and desirable properties.

Transatlantic strategic convergence on China and the scramble for critical minerals

Purpose The purpose of this paper is to investigate the trend of transatlantic strategic convergence and policy coordination in response to Chinese trade practices and technological competition, specifically in the critical minerals sector. Design/methodology/approach The research draws on primary and secondary source material to identify evidence of and examine the drivers, manifestations and prospects for effective US-European efforts to advance the shared aim of reducing vulnerabilities in critical minerals supply chains. Findings The interests of the USA and Europe would be best served by prioritizing their own security, diversification and resilience strategies while seeking areas of common ground and constructive engagement with China. Research limitations/implications The research offers a fresh perspective on the growing alignment and persistent gaps in US and European perspectives on China’s rising influence and assertive behavior. Originality/value The research highlights the vital role of critical minerals in national security, economic competitiveness, technological advancement and sustainable resource management. It underscores the shared recognition on both sides of the Atlantic that securing a stable supply of critical minerals – essential for maintaining strategic capabilities, driving innovation and ensuring long-term economic prosperity – necessitates tighter transatlantic coordination as well as constructive engagement with China.

Correlations between alignment gaps and nucleotide substitution or amino acid replacement

To assess the conventional treatment in evolutionary inference of alignment gaps as missing data, we propose a simple nonparametric test of the null hypothesis that the locations of alignment gaps are independent of the nucleotide substitution or amino acid replacement process. When we apply the test to 1,390 protein alignments that are informed by protein tertiary structure and use a 5% significance level, the null hypothesis of independence between amino acid replacement and gap location is rejected for ∼65% of datasets. Via simulations that include substitution and insertion-deletion, we show that the test performs well with true alignments. When we simulate according to the null hypothesis and then apply the test to optimal alignments that are inferred by each of four widely used software packages, the null hypothesis is rejected too frequently. Via further simulations and analyses, we show that the overly frequent rejections of the null hypothesis are not solely due to weaknesses of widely used software for finding optimal alignments. Instead, our evidence suggests that optimal alignments are unrepresentative of true alignments and that biased evolutionary inferences may result from relying upon individual optimal alignments.

Quality of Pre-School Teacher Education in Ethiopia and its Implication for Quality Learning Outcomes

This study looks at the quality of preschool teacher education in Ethiopia in view of three basic components: curriculum relevance, profiles of teacher educators, and the selection and recruitment of candidates. The study adopted a case study design guided by competency-based teacher development theory and collected data through documentary analysis (the curriculum and recruitment guideline), and interviews of five professionals. The findings showed that the preschool teacher education curriculum has alignment gaps in four major aspects: (a) the preschool teacher education curriculum focused on subject area contents rather than on holistic child development, (b) the preschool teacher education curriculum overlooked motor skills as well as socio-emotional development categories, and (c) languages of instructions at preschool teacher education and preschool level are different (English and mother tongue respectively). Besides, invited professionals from other departments offer 36 of the 42 courses but lacked appropriate professional orientation and experiences to prepare the less capable candidates admitted to the program. Accordingly, policy intervention to make appropriate amendments in the curriculum, staff profiles and practicum components, and further research on views of graduates and relevant stakeholders were identified as areas of further endeavors.

CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments.

BackgroundThroughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce.ResultsWe present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is designed with an emphasis on solving specific and common alignment problems and on providing transparency to the user.ConclusionCIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options. This tool can be used to fine-tune alignments for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs.

Dysgu: efficient structural variant calling using short or long reads.

Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), although paired-end sequencing offers better scalability. Here, we present dysgu, which calls SVs or indels using paired-end or long reads. Dysgu detects signals from alignment gaps, discordant and supplementary mappings, and generates consensus contigs, before classifying events using machine learning. Additional SVs are identified by remapping of anomalous sequences. Dysgu outperforms existing state-of-the-art tools using paired-end or long-reads, offering high sensitivity and precision whilst being among the fastest tools to run. We find that combining low coverage paired-end and long-reads is competitive in terms of performance with long-reads at higher coverage values.

Measuring Phylogenetic Information of Incomplete Sequence Data.

Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the effective sequence length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification. [Fisher information; gaps; insertion; deletion; indel; model adequacy; goodness-of-fit test; sequence alignment.].

Component placement accuracy in two generations of handheld robotics-assisted knee arthroplasty.

Total knee arthroplasty (TKA) is the gold standard for treatment of end-stage osteoarthritis. Previous studies have shown that successful outcomes following TKA depend on accurate implant alignment and soft tissue balancing. Robotic-assisted TKA have demonstrated improved accuracy in component placement and have been associated with better outcomes and patient satisfaction. This study aims to report on the execution accuracy of two generations of handheld robotic-assisted surgical systems. This was a retrospective analysis of TKA procedures with two sequential generations of the same handheld robotic-assisted surgical system. Intra-operative data captured included pre-operative limb deformity, limb axes, range of motion, kinematic balance, and the resulting plan for component placement in three-dimensional space. Patients were stratified based on their preoperative coronal lower limb mechanical alignment (> 3° varus, < 3° varus, < 3° valgus, and ≥ 3° valgus). Measurements of component placement (overall lower limb alignment, medial and lateral flexion gaps, and tibial and femoral resection depths) were assessed using descriptive statistics. A total of 435 patients were included and stratified based on preoperative lower limb alignment: 229 with ≥ 3° varus, 78 with varus < 3° and 58 with valgus < 3°, and 70 with valgus > 3°. The mean difference between planned and achieved alignment in the lower limb valgus patients was < 1° across all groups. Mean differences between planned and achieved medial flexion gap was higher in the > 3° subgroup in the varus patient cohort ([< 3°]: 1.15 ± 1.92 vs. [> 3°]: 1.90 ± 2.57); this value was higher in the < 3° subgroup for valgus patients ([< 3°]: 1.34 ± 1.83 vs. [> 3°]: 0.956 ± 1.65). Average resection depth ranged from 9.46 to 10.4mm in the posterior medial femur, 9.25 to 9.95mm in the posterior lateral femur, 7.45 to 8.79mm in the distal medial femur, 8.22 to 9.18mm in the distal lateral femur, 6.70 to 7.07mm in the medial tibial condyle and 6.40 to 7.19mm in the lateral tibial condyle. Non-inferiority testing demonstrated the newer generation is non-inferior to the older generation. Robotic-assisted knee replacement using handheld image-free systems is able to maintain accuracy of component placement. Further investigation of patient reported outcomes as well as long-term implant longevity are needed.

A 313 plastome phylogenomic analysis of Pooideae: Exploring relationships among the largest subfamily of grasses

In this study, we analyzed 313 plastid genomes (plastomes) of Poaceae with a focus on expanding our current knowledge of relationships among the subfamily Pooideae, which represented over half the dataset (164 representatives). In total, 47 plastomes were sequenced and assembled for this study. This is the largest study of its kind to include plastome-level data, to not only increase sampling at both the taxonomic and molecular levels with the aim of resolving complex and reticulate relationships, but also to analyze the effects of alignment gaps in large-scale analyses, as well as explore divergences in the subfamily with an expanded set of 14 accepted grass fossils for more accurate calibrations and dating. Incorporating broad systematic assessments of Pooideae taxa conducted by authors within the last five years, we produced a robust phylogenomic reconstruction for the subfamily, which included all but two supergeneric taxa (Calothecinae and Duthieeae).We further explored how including alignment gaps in plastome analyses oftentimes can produce incorrect or misinterpretations of complex or reticulate relationships among taxa of Pooideae. This presented itself as consistently changing relationships at specific nodes for different stripping thresholds (percentage-based removal of gaps per alignment column). Our summary recommendation for large-scale genomic plastome datasets is to strip alignment columns of all gaps to increase pairwise identity and reduce errant signal from poly A/T bias. To do this we used the “mask alignment” tool in Geneious software. Finally, we determined an overall divergence age for Pooideae of roughly 84.8 Mya, which is in line with, but slightly older than most recent estimates.

Phylogeny-Aware Alignment with PRANK and PAGAN.

Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary homology and proteins' structural similarity are not the same and sequence alignments generated with methods designed for structural matching can be seriously misleading in comparative and phylogenetic analyses. The phylogeny-aware alignment algorithm implemented in the program PRANK has been shown to produce good alignments for evolutionary inferences. Unlike other alignment programs, PRANK makes use of phylogenetic information to distinguish alignment gaps caused by insertions or deletions and, thereafter, handles the two types of events differently. As a by-product of the correct handling of insertions and deletions, PRANK can provide the inferred ancestral sequences as a part of the output and mark the alignment gaps differently depending on their origin in insertion or deletion events. As the algorithm infers the evolutionary history of the sequences, PRANK can be sensitive to errors in the guide phylogeny and violations on the underlying assumptions about the origin and patterns of gaps. To mitigate the effects of such model violations, the phylogeny-aware alignment algorithm has been re-implemented in program PAGAN. By using sequence graphs, PAGAN can model and accumulate evidence from more complex gap structures than PRANK does, and incorporate this uncertainty in the inferred ancestral sequences. These issues are discussed in detail below and practical advice is provided for the use of PRANK and PAGAN in evolutionary analysis. The two software packages can be downloaded from http://wasabiapp.org/software .

Result of posteromedial capsule and superficial medial collateral ligament release on gap and alignment in total knee arthroplasty in varusknee deformity by computer assisted surgery measurement: a retrospective stud

Soft tissue release and gap balancing in total knee arthroplasty (TKA) are important issue and lack of conclusive result. We performed posteromedial capsule (PMC) and superficial medial collateral ligament (sMCL) release by preservation of anterior attachment of pes anserine. Gaps and alignment were recorded by computer assisted surgery measurement.Results:T: The mean correction of varus deformity after PMC release and sMCL release were 4.88 ± 2.82° and 3.39 ± 1.7 respectively with the mean FC after PMC and sMCL release correction of 5.57 ± 3.5 and 1.34 ± 2.9° respectively. The mean medial gap changes on full extension after PMC and sMCL release was 1.83 ± 1.39 and 1.67 ± 1.04 mm. respectively with the mean medial gaps at 90 degree flexion after PMC and sMCL release changes of 0.73 ± 0.9 and 5.14 ± 2.11 mm. respectively. The mean lateral gap changes on extension after PMC and sMCL release were -1.3 ± 1.83 and -1.1 ± 1.6 mm. respectively with the mean lateral gaps at 90 degree flexion after PMC and sMCL release changes of -0.19 ± 1.03 and 0.06 ± 1.75 mm. here were 21 patients (16 female and 5 male) with mean age of 68 (48-78) years. The mean body mass index was 28.49 (20.70 – 39.95) kg/m2. The mean preoperative hip-knee-ankle angle was varus 8.12 (3.5-16.0) degrees with mean flexion contracture of 11.3 (3.5-16.0) degrees. Sixteen knees were implanted with Fixed bearing knee prosthesis and five knees were implanted with Mobile bearing knee prosthesis (Table.1). We performed PMC release in all patients, and combined PMC and sMCL release in fourteen patients. The mean correction of varus deformity after PM release and sMCL release were 4.88 ± 2.82 and 3.39 ± 1.7 degrees respectively. While the mean correction of flexion contracture after PMC release and sMCL release were 5.57 ± 3.5 and 1.34 ± 2.9 degrees respectively (Fig.8). The mean medial gaps change on extension after PMC and sMCL release were 1.83 ± 1.39 and 1.67 ± 1.04 mm. respectively. The mean medial gaps change at 90 degree flexion after PMC and sMCL release were 0.73 ± 0.9 and 5.14 ± 2.11 mm. respectively (Fig.9). The mean lateral gaps change on extension after PMC and sMCL release were 1.3 ± 1.83 and -1.1 ± 1.6 mm. respectively. The mean lateral gaps change at 90 degree flexion after PMC and sMCL release were -0.19 ± 1.03 and 0.06 ± 1.75 mm. (Fig.9). There is no instability of knee after PMC and sMCL release.Materials and Methods:Twenty one patient had been operated on. TKA with computer assisted surgery was performed using PMC and sMCL release by preservation of anterior attachment of pes anserine. Alignment, medial and lateral gaps were measured by computer assisted surgery. The mean age was 68 (48-78) years with the mean preoperative hip-kneeankle angle of 8.12 (3.5-16.0) degrees and the mean flexion contracture (FC) of 11.3 (3.516.0) degrees.Conclusion:We believe that sMCL release with preservation of anterior attachment of pes anserinus in total knee arthroplasty has additional effect on varus knee correction after PMC release without creation of knee instability.

Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps

AbstractIn Poaceae there is an evolutionary radiation of c. 5000 species called the ‘PACMAD’ grasses. Two hypotheses explain deep PACMAD relationships: the ‘aristidoid sister’ and the ‘panicoid sister’ hypotheses. In each case, the named subfamily is sister to all other taxa. These hypotheses were investigated with data partitions from plastid genomes (plastomes) of 169 grasses including five newly sequenced aristidoids. Plastomes were analysed 40 times with successive addition of more gapped positions introduced by sequence alignment, until all such positions were included. Alignment gaps include low complexity, AT-rich regions. Without gaps, the panicoid sister hypothesis (P(ACMAD)) was moderately supported, but as gaps were gradually added into the input matrix, the topology and support values fluctuated through a transition zone with stripping thresholds from 2–11% until a weakly supported aristidoid sister topology was retrieved. Support values for the aristidoid sister topology then rose and plateaued for remaining analyses until all gaps were allowed. The fact that the aristidoid sister hypothesis was retrieved largely when gapped positions were included suggests that this result might be artefactual. Knowledge of the deep PACMAD topology explicitly impacts our understanding of the radiation of PACMAD grasses into open habitats.

Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13.

We report the results of residue-residue contact prediction of a new pipeline built purely on the learning of coevolutionary features in the CASP13 experiment. For a query sequence, the pipeline starts with the collection of multiple sequence alignments (MSAs) from multiple genome and metagenome sequence databases using two complementary Hidden Markov Model (HMM)-based searching tools. Three profile matrices, built on covariance, precision, and pseudolikelihood maximization respectively, are then created from the MSAs, which are used as the input features of a deep residual convolutional neural network architecture for contact-map training and prediction. Two ensembling strategies have been proposed to integrate the matrix features through end-to-end training and stacking, resulting in two complementary programs called TripletRes and ResTriplet, respectively. For the 31 free-modeling domains that do not have homologous templates in the PDB, TripletRes and ResTriplet generated comparable results with an average accuracy of 0.640 and 0.646, respectively, for the top L/5 long-range predictions, where 71% and 74% of the cases have an accuracy above 0.5. Detailed data analyses showed that the strength of the pipeline is due to the sensitive MSA construction and the advanced strategies for coevolutionary feature ensembling. Domain splitting was also found to help enhance the contact prediction performance. Nevertheless, contact models for tail regions, which often involve a high number of alignment gaps, and for targets with few homologous sequences are still suboptimal. Development of new approaches where the model is specifically trained on these regions and targets might help address these problems.

Short Communication: Species identity and taxonomical position of selected species of Annonaceae based on trnL molecular marker

Abstract. Lestari DA, Azrianingsih R. 2019. Species identity and taxonomical position of selected species of Annonaceae based on trnL molecular marker. Biodiversitas 20: 1012-1019. Identification based on morphological characters could be difficult when some characters are not visible. The absence of some morphological characters could effect for identification of species identity and taxonomical position of the species. Confirmation by the DNA data is needed to support species identification. The sequence was used in this research is trnL intron as non-coding sequence DNA, based on chloroplast DNA. The research aimed to estimate of species identity and determine of taxonomical position of species of Annonaceae based on trnL sequences. Methods were used through steps of DNA extraction, DNA amplification, DNA sequencing, and data analysis to selected species of Annonaceae from Purwodadi Botanic Garden (PBG), the trnL intron sequences of 10 Annonaceae species from GenBank database and two species of Magnoliaceae as out-group. Results showed that trnL sequence as non-coding gene explains the different groupings with the previous groupings in Annonaceae to this observed species. trnL sequence can estimate of species identity as much as 30%, caused by changes of nucleotide bases from mutation and missing data. Polymorphism of DNA sequences showed that 61.18% sites as conserved region, 24.05% sites as polymorphic variation and 14.76% sites as alignment gaps. Oxymitra sp. is in group (monophyletic) with Mitrephora javanica because they are genetically in close relationship (Uvariae tribes and Annonoideae sub-family), Popowia sp. is in group with Orophea enterocarpa, because they are genetically in close relationship (Miliuseae tribes and Malmeoideae sub-family).

First principles study of hBN-AlN short-period superlattice heterostructures

We report a theoretical study of the structural, electronic, and optical properties of hBN-AlN superlattice (SL) heterostructures using a first-principles approach based on standard and hybrid density functional theory. We consider a short-period (L &amp;lt; 10 nm) SL and find that its properties depend strongly on the AlN layer thickness LAlN. For LAlN≲1 nm, AlN stabilizes into the hexagonal phase and the SL displays insulating behavior with type II interface band alignment and optical gaps as small as 5.2 eV. The wurtzite phase is formed for thicker AlN layers. In these cases, built-in electric fields lead to the formation of polarization compensating charges as well as two-dimensional conductive behavior for electronic transport along interfaces. We also find defect-like states localized at interfaces which are optically active in the visible range.

Genetic Variability and Relationship of Banana Cultivars (Musa L.) From East Java, Indonesia based on the Internal Transcribed Spacer Region nrDNA Sequences

A genetic variability and relationship study subjected to 41 banana cultivars from East Java based on nrDNA sequences of the ITS region was conducted. It would be useful to consider the genomic identification, genetic conservation strategy, and for further banana improvement. ITSL and ITS4 primers were used to amplify the ITS region. Results show that the ITS region DNA sequences length of 41 banana cultivars examined varied from 631 bp to 651 bp. It showed high variability with conservation level G+C content of 62.79%. Total aligned and selected ITS region DNA sequences was 656 bp comprising 346 positions (52.74%) as conserved region, 223 positions (33.99%) as variable sites (polymorphic) and 87 positions (13.26%) alignment gaps. About 143 positions (64.13%) of the variable positions were potentially parsimony informative and 80 positions (35.87%) were singleton variables. The singletone variation sequences spesific to certain banana cultivars may be proposed as identification barcodes. The haplotype diversity was very rich (Hd=1.00), resulted 41 haplotypes with none of haplogroup. Haplotype distribution map revealed the lineage pattern of banana cultivars from East Java. They were presummably derived from common ancestors and the same population in East Java mainland which then experienced an evolution process, dispersed by human migration both in and out, and became isolated to the islands. Genetic relationship reconstruction using NJ algorithm resulted in a tree and classification better than MP algorithm. It was clustered according to its geomic group, into 3 main clades i.e. AA/AAA, AAB and ABB. The ITS region nrDNA sequences was proven powerful in classifying until cultivar level of bananas. All 41 banana cultivars examined are recommended for genetics conservation.

Large process-dependent variations in band alignment and interface band gaps of Cu2ZnSnS4/CdS solar cells

Electron–hole recombination at the Cu2ZnSnS4/CdS interface is believed to play a major role in limiting the efficiency of Cu2ZnSnS4 solar cells. In this work, we experimentally determine detailed Cu2ZnSnS4/CdS interface band diagrams as a function of process conditions, and correlate them to chemical processes occurring during interface formation and subsequent post-annealing. The newly devised experimental method involves a combination of photoemission spectroscopy and spectroscopic ellipsometry. Our measurements reveal that, under most process conditions, the band gaps of both Cu2ZnSnS4 and CdS decrease by several hundred meV near the interface. Furthermore, interface band bending and conduction band offsets are highly process-dependent and roughly correlated to the amount of chemical interdiffusion. The interface electronic properties are found to be unfavorable under all process conditions studied in this work, either due to a cliff-like conduction band offset, or to substantial band gap narrowing in Cu2ZnSnS4, or to both effects. According to the present study, the least harmful process conditions for the interface electronic properties are a low CdS deposition temperature without post-annealing. Even in such a case, a minimum open circuit voltage loss of 230 mV is expected due to interface- or near-interface recombination.

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.

Validation of Splicing Events in Transcriptome Sequencing Data.

Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis.

CoeViz: a web-based tool for coevolution analysis of protein residues.

BackgroundProteins generally perform their function in a folded state. Residues forming an active site, whether it is a catalytic center or interaction interface, are frequently distant in a protein sequence. Hence, traditional sequence-based prediction methods focusing on a single residue (or a short window of residues) at a time may have difficulties in identifying and clustering the residues constituting a functional site, especially when a protein has multiple functions. Evolutionary information encoded in multiple sequence alignments is known to greatly improve sequence-based predictions. Identification of coevolving residues further advances the protein structure and function annotation by revealing cooperative pairs and higher order groupings of residues.ResultsWe present a new web-based tool (CoeViz) that provides a versatile analysis and visualization of pairwise coevolution of amino acid residues. The tool computes three covariance metrics: mutual information, chi-square statistic, Pearson correlation, and one conservation metric: joint Shannon entropy. Implemented adjustments of covariance scores include phylogeny correction, corrections for sequence dissimilarity and alignment gaps, and the average product correction. Visualization of residue relationships is enhanced by hierarchical cluster trees, heat maps, circular diagrams, and the residue highlighting in protein sequence and 3D structure. Unlike other existing tools, CoeViz is not limited to analyzing conserved domains or protein families and can process long, unstructured and multi-domain proteins thousands of residues long. Two examples are provided to illustrate the use of the tool for identification of residues (1) involved in enzymatic function, (2) forming short linear functional motifs, and (3) constituting a structural domain.ConclusionsCoeViz represents a practical resource for a quick sequence-based protein annotation for molecular biologists, e.g., for identifying putative functional clusters of residues and structural domains. CoeViz also can serve computational biologists as a resource of coevolution matrices, e.g., for developing machine learning-based prediction models. The presented tool is integrated in the POLYVIEW-2D server (http://polyview.cchmc.org/) and available from resulting pages of POLYVIEW-2D.