Exact p-value calculation for XCorr scoring of high-resolution MS/MS data.

Exact p-value (XPV)-based methods for dot product-like score functions-such as the XCorr score implemented in Tide, SEQUEST, Comet or shared peak count-based scoring in MSGF+ and ASPV-provide a fairly good calibration for peptide-spectrum-match (PSM) scoring in database searching-based MS/MS spectrum data identification. Unfortunately, standard XPV methods, in practice, cannot handle high-resolution fragmentation data produced by state-of-the-art mass spectrometers because having smaller bins increases the number of fragment matches that are assigned to incorrect bins and scored improperly. In this article, we present an extension of the XPV method, called the high-resolution exact p-value (HR-XPV) method, which can be used to calibrate PSM scores of high-resolution MS/MS spectra obtained with dot product-like scoring such as the XCorr. The HR-XPV carries remainder masses throughout the fragmentation, allowing them to greatly increase the number of fragments that are properly assigned to the correct bin and, thus, taking advantage of high-resolution data. Using four mass spectrometry data sets, our experimental results demonstrate that HR-XPV produces well-calibrated scores, which in turn results in more trusted spectrum annotations at any false discovery rate level.

Human pancreatic ductal organoids with controlled polarity provide a novel ex vivo tool to study epithelial cell physiology.

Epithelial ion and fluid secretion determine the physiological functions of a broad range of organs, such as the lung, liver, or pancreas. The molecular mechanism of pancreatic ion secretion is challenging to investigate due to the limited access to functional human ductal epithelia. Patient-derived organoids may overcome these limitations, however direct accessibility of the apical membrane is not solved. In addition, due to the vectorial transport of ions and fluid the intraluminal pressure in the organoids is elevated, which may hinder the study of physiological processes. To overcome these, we developed an advanced culturing method for human pancreatic organoids based on the removal of the extracellular matrix that induced an apical-to-basal polarity switch also leading to reversed localization of proteins with polarized expression. The cells in the apical-out organoids had a cuboidal shape, whereas their resting intracellular Ca2+ concentration was more consistent compared to the cells in the apical-in organoids. Using this advanced model, we demonstrated the expression and function of two novel ion channels, the Ca2+ activated Cl- channel Anoctamin 1 (ANO1) and the epithelial Na+ channel (ENaC), which were not considered in ductal cells yet. Finally, we showed that the available functional assays, such as forskolin-induced swelling, or intracellular Cl- measurement have improved dynamic range when performed with apical-out organoids. Taken together our data suggest that polarity-switched human pancreatic ductal organoids are suitable models to expand our toolset in basic and translational research.

Efficient Indexing of Peptides for Database Search Using Tide.

The first step in the analysis of protein tandem mass spectrometry data typically involves searching the observed spectra against a protein database. During database search, the search engine must digest the proteins in the database into peptides, subject to digestion rules that are under user control. The choice of these digestion parameters, as well as selection of post-translational modifications (PTMs), can dramatically affect the size of the search space and hence the statistical power of the search. The Tide search engine separates the creation of the peptide index from the database search step, thereby saving time by allowing a peptide index to be reused in multiple searches. Here we describe an improved implementation of the indexing component of Tide that consumes around four times less resources (CPU and RAM) than the previous version and can generate arbitrarily large peptide databases, limited by only the amount of available disk space. We use this improved implementation to explore the relationship between database size and the parameters controlling digestion and PTMs, as well as database size and statistical power. Our results can help guide practitioners in proper selection of these important parameters.

The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.

The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments since 2014. We begin with empirical results demonstrating our recently implemented speedups to the Tide search engine. Other new features include a new score function in Tide, two new confidence estimation procedures, as well as three new tools: Param-medic for estimating search parameters directly from mass spectrometry data, Kojak for searching cross-linked mass spectra, and DIAmeter for searching data independent acquisition data against a sequence database.

Thermally Induced Solid-Phase Quasi-Intramolecular Redox Reactions of [Hexakis(urea-O)iron(III)] Permanganate: An Easy Reaction Route to Prepare Potential (Fe,Mn)Ox Catalysts for CO2 Hydrogenation.

Research on new reaction routes and precursors to prepare catalysts for CO2 hydrogenation has enormous importance. Here, we report on the preparation of the permanganate salt of the urea-coordinated iron(III), [hexakis(urea-O)iron(III)]permanganate ([Fe(urea-O)6](MnO4)3) via an affordable synthesis route and preliminarily demonstrate the catalytic activity of its (Fe,Mn)Ox thermal decomposition products in CO2 hydrogenation. [Fe(urea-O)6](MnO4)3 contains O-coordinated urea ligands in octahedral propeller-like arrangement around the Fe3+ cation. There are extended hydrogen bond interactions between the permanganate ions and the hydrogen atoms of the urea ligands. These hydrogen bonds serve as reaction centers and have unique roles in the solid-phase quasi-intramolecular redox reaction of the urea ligand and the permanganate anion below the temperature of ligand loss of the complex cation. The decomposition mechanism of the urea ligand (ammonia elimination with the formation of isocyanuric acid and biuret) has been clarified. In an inert atmosphere, the final thermal decomposition product was manganese-containing wuestite, (Fe,Mn)O, at 800 °C, whereas in ambient air, two types of bixbyite (Fe,Mn)2O3 as well as jacobsite (Fe,Mn)T-4(Fe,Mn)OC-62O4), with overall Fe to Mn stoichiometry of 1:3, were formed. These final products were obtained regardless of the different atmospheres applied during thermal treatments up to 350 °C. Disordered bixbyite formed first with inhomogeneous Fe and Mn distribution and double-size supercell and then transformed gradually into common bixbyite with regular structure (and with 1:3 Fe to Mn ratio) upon increasing the temperature and heating time. The (Fe,Mn)Ox intermediates formed under various conditions showed catalytic effect in the CO2 hydrogenation reaction with <57.6% CO2 conversions and <39.3% hydrocarbon yields. As a mild solid-phase oxidant, hexakis(urea-O)iron(III) permanganate, was found to be selective in the transformation of (un)substituted benzylic alcohols into benzaldehydes and benzonitriles.

Challenges and Opportunities of Implementing Data Fusion in Process Analytical Technology-A Review.

The release of the FDA's guidance on Process Analytical Technology has motivated and supported the pharmaceutical industry to deliver consistent quality medicine by acquiring a deeper understanding of the product performance and process interplay. The technical opportunities to reach this high-level control have considerably evolved since 2004 due to the development of advanced analytical sensors and chemometric tools. However, their transfer to the highly regulated pharmaceutical sector has been limited. To this respect, data fusion strategies have been extensively applied in different sectors, such as food or chemical, to provide a more robust performance of the analytical platforms. This survey evaluates the challenges and opportunities of implementing data fusion within the PAT concept by identifying transfer opportunities from other sectors. Special attention is given to the data types available from pharmaceutical manufacturing and their compatibility with data fusion strategies. Furthermore, the integration into Pharma 4.0 is discussed.

Deep Convolutional Neural Networks Help Scoring Tandem Mass Spectrometry Data in Database-Searching Approaches.

Spectrum annotation is a challenging task due to the presence of unexpected peptide fragmentation ions as well as the inaccuracy of the detectors of the spectrometers. We present a deep convolutional neural network, called Slider, which learns an optimal feature extraction in its kernels for scoring mass spectrometry (MS)/MS spectra to increase the number of spectrum annotations with high confidence. Experimental results using publicly available data sets show that Slider can annotate slightly more spectra than the state-of-the-art methods (BoltzMatch, Res-EV, Prosit), albeit 2-10 times faster. More interestingly, Slider provides only 2-4% fewer spectrum annotations with low-resolution fragmentation information than other methods with high-resolution information. This means that Slider can exploit nearly as much information from the context of low-resolution spectrum peaks as the high-resolution fragmentation information can provide for other scoring methods. Thus, Slider can be an optimal choice for practitioners using old spectrometers with low-resolution detectors.

Demonstration of age-related blood-brain barrier disruption and cerebromicrovascular rarefaction in mice by longitudinal intravital two-photon microscopy and optical coherence tomography.

Age-related blood-brain barrier (BBB) disruption and cerebromicrovascular rarefaction contribute importantly to the pathogenesis of both vascular cognitive impairment and dementia (VCID) and Alzheimer's disease (AD). Recent advances in geroscience research enable development of novel interventions to reverse age-related alterations of the cerebral microcirculation for prevention of VCID and AD. To facilitate this research, there is an urgent need for sensitive and easy-to-adapt imaging methods that enable longitudinal assessment of changes in BBB permeability and brain capillarization in aged mice and that could be used in vivo to evaluate treatment efficiency. To enable longitudinal assessment of changes in BBB permeability in aged mice equipped with a chronic cranial window, we adapted and optimized two different intravital two-photon imaging approaches. By assessing relative fluorescence changes over the baseline within a volume of brain tissue, after qualitative image subtraction of the brain microvasculature, we confirmed that, in 24-mo-old C57BL/6J mice, cumulative permeability of the microvessels to fluorescent tracers of different molecular masses (0.3 to 40 kDa) is significantly increased compared with that of 5-mo-old mice. Real-time recording of vessel cross-sections showed that apparent solute permeability of single microvessels is significantly increased in aged mice vs. young mice. Cortical capillary density, assessed both by intravital two-photon microscopy and optical coherence tomography was also decreased in aged mice vs. young mice. The presented methods have been optimized for longitudinal (over the period of 36 wk) in vivo assessment of cerebromicrovascular health in preclinical geroscience research.NEW & NOTEWORTHY Methods are presented for longitudinal detection of age-related increase in blood-brain barrier permeability and microvascular rarefaction in the mouse cerebral cortex by intravital two-photon microscopy and optical coherence tomography.

Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics.

MOTIVATION: The discrimination ability of score functions to separate correct from incorrect peptide-spectrum-matches in database-searching-based spectrum identification is hindered by many superfluous peaks belonging to unexpected fragmentation ions or by the lacking peaks of anticipated fragmentation ions. RESULTS: Here, we present a new method, called BoltzMatch, to learn score functions using a particular stochastic neural networks, called restricted Boltzmann machines, in order to enhance their discrimination ability. BoltzMatch learns chemically explainable patterns among peak pairs in the spectrum data, and it can augment peaks depending on their semantic context or even reconstruct lacking peaks of expected ions during its internal scoring mechanism. As a result, BoltzMatch achieved 50% and 33% more annotations on high- and low-resolution MS2 data than XCorr at a 0.1% false discovery rate in our benchmark; conversely, XCorr yielded the same number of spectrum annotations as BoltzMatch, albeit with 4-6 times more errors. In addition, BoltzMatch alone does yield 14% more annotations than Prosit (which runs with Percolator), and BoltzMatch with Percolator yields 32% more annotations than Prosit at 0.1% FDR level in our benchmark. AVAILABILITY AND IMPLEMENTATION: BoltzMatch is freely available at: https://github.com/kfattila/BoltzMatch. CONTACT: akerteszfarkas@hse.ru. SUPPORTING INFORMATION: Supplementary data are available at Bioinformatics online.

Comparison of Amorphous Solid Dispersions of Spironolactone Prepared by Spray Drying and Electrospinning: The Influence of the Preparation Method on the Dissolution Properties.

This research aimed to compare two solvent-based methods for the preparation of amorphous solid dispersions (ASDs) made up of poorly soluble spironolactone and poly(vinylpyrrolidone-co-vinyl acetate). The same apparatus was used to produce, in continuous mode, drug-loaded electrospun (ES) and spray-dried (SD) materials from dichloromethane and ethanol-containing solutions. The main differences between the two preparation methods were the concentration of the solution and application of high voltage. During electrospinning, a solution with a higher concentration and high voltage was used to form a fibrous product. In contrast, a dilute solution and no electrostatic force were applied during spray drying. Both ASD products showed an amorphous structure according to differential scanning calorimetry and X-ray powder diffraction results. However, the dissolution of the SD sample was not complete, while the ES sample exhibited close to 100% dissolution. The polarized microscopy images and Raman microscopy mapping of the samples highlighted that the SD particles contained crystalline traces, which can initiate precipitation during dissolution. Investigation of the dissolution media with a borescope made the precipitated particles visible while Raman spectroscopy measurements confirmed the appearance of the crystalline active pharmaceutical ingredient. To explain the micro-morphological differences, the shape and size of the prepared samples, the evaporation rate of residual solvents, and the influence of the electrostatic field during the preparation of ASDs had to be considered. This study demonstrated that the investigated factors have a great influence on the dissolution of the ASDs. Consequently, it is worth focusing on the selection of the appropriate ASD preparation method to avoid the deterioration of dissolution properties due to the presence of crystalline traces.

Solid-Phase Quasi-Intramolecular Redox Reaction of [Ag(NH3)2]MnO4: An Easy Way to Prepare Pure AgMnO2.

Two monoclinic polymorphs of [Ag(NH3)2]MnO4 containing a unique coordination mode of permanganate ions were prepared, and the high-temperature polymorph was used as a precursor to synthesize pure AgMnO2. The hydrogen bonds between the permanganate ions and the hydrogen atoms of ammonia were detected by IR spectroscopy and single-crystal X-ray diffraction. Under thermal decomposition, these hydrogen bonds induced a solid-phase quasi-intramolecular redox reaction between the [Ag(NH3)2]+ cation and MnO4- anion even before losing the ammonia ligand or permanganate oxygen atom. The polymorphs decomposed into finely dispersed elementary silver, amorphous MnOx compounds, and H2O, N2 and NO gases. Annealing the primary decomposition product at 573 K, the metallic silver reacted with the manganese oxides and resulted in the formation of amorphous silver manganese oxides, which started to crystallize only at 773 K and completely transformed into AgMnO2 at 873 K.

Nuclear architecture dictates HIV-1 integration site selection.

Long-standing evidence indicates that human immunodeficiency virus type 1 (HIV-1) preferentially integrates into a subset of transcriptionally active genes of the host cell genome. However, the reason why the virus selects only certain genes among all transcriptionally active regions in a target cell remains largely unknown. Here we show that HIV-1 integration occurs in the outer shell of the nucleus in close correspondence with the nuclear pore. This region contains a series of cellular genes, which are preferentially targeted by the virus, and characterized by the presence of active transcription chromatin marks before viral infection. In contrast, the virus strongly disfavours the heterochromatic regions in the nuclear lamin-associated domains and other transcriptionally active regions located centrally in the nucleus. Functional viral integrase and the presence of the cellular Nup153 and LEDGF/p75 integration cofactors are indispensable for the peripheral integration of the virus. Once integrated at the nuclear pore, the HIV-1 DNA makes contact with various nucleoporins; this association takes part in the transcriptional regulation of the viral genome. These results indicate that nuclear topography is an essential determinant of the HIV-1 life cycle.

Effect of ivabradine in heart failure: a meta-analysis of heart failure patients with reduced versus preserved ejection fraction.

In clinical trials of heart failure reduced ejection fraction (HFrEF), ivabradine seemed to be an effective heart rate lowering agent associated with lower risk of cardiovascular death. In contrast, ivabradine failed to improve cardiovascular outcomes in heart failure preserved ejection fraction (HFpEF) despite the significant effect on heart rate. This meta-analysis is the first to compare the effects of ivabradine on heart rate and mortality parameters in HFpEF versus HFrEF. We screened three databases: PubMed, Embase, and Cochrane Library. The outcomes of these studies were mortality, reduction in heart rate, and left ventricular function improvement. We compared the efficacy of ivabradine treatment in HFpEF versus HFrEF. Heart rate analysis of pooled data showed decrease in both HFrEF (-17.646 beats/min) and HFpEF (-11.434 beats/min), and a tendency to have stronger bradycardic effect in HFrEF (p = 0.094) in randomized clinical trials. Left ventricular ejection fraction analysis revealed significant improvement in HFrEF (5.936, 95% CI: [4.199-7.672], p < 0.001) when compared with placebo (p < 0.001). We found that ivabradine significantly improves left ventricular performance in HFrEF, at the same time it exerts a tendency to have improved bradycardic effect in HFrEF. These disparate effects of ivabradine and the higher prevalence of non-cardiac comorbidities in HFpEF may explain the observed beneficial effects in HFrEF and the unchanged outcomes in HFpEF patients after ivabradine treatment.

Astrocyte Ca2+ Waves and Subsequent Non-Synchronized Ca2+ Oscillations Coincide with Arteriole Diameter Changes in Response to Spreading Depolarization.

Spreading depolarization (SD) is a wave of mass depolarization that causes profound perfusion changes in acute cerebrovascular diseases. Although the astrocyte response is secondary to the neuronal depolarization with SD, it remains to be explored how glial activity is altered after the passage of SD. Here, we describe post-SD high frequency astrocyte Ca2+ oscillations in the mouse somatosensory cortex. The intracellular Ca2+ changes of SR101 labeled astrocytes and the SD-related arteriole diameter variations were simultaneously visualized by multiphoton microscopy in anesthetized mice. Post-SD astrocyte Ca2+ oscillations were identified as Ca2+ events non-synchronized among astrocytes in the field of view. Ca2+ oscillations occurred minutes after the Ca2+ wave of SD. Furthermore, fewer astrocytes were involved in Ca2+ oscillations at a given time, compared to Ca2+ waves, engaging all astrocytes in the field of view simultaneously. Finally, our data confirm that astrocyte Ca2+ waves coincide with arteriolar constriction, while post-SD Ca2+ oscillations occur with the peak of the SD-related vasodilation. This is the first in vivo study to present the post-SD astrocyte Ca2+ oscillations. Our results provide novel insight into the spatio-temporal correlation between glial reactivity and cerebral arteriole diameter changes behind the SD wavefront.

Cerebral Pericytes and Endothelial Cells Communicate through Inflammasome-Dependent Signals.

By upregulation of cell adhesion molecules and secretion of proinflammatory cytokines, cells of the neurovascular unit, including pericytes and endothelial cells, actively participate in neuroinflammatory reactions. As previously shown, both cell types can activate inflammasomes, cerebral endothelial cells (CECs) through the canonical pathway, while pericytes only through the noncanonical pathway. Using complex in vitro models, we demonstrate here that the noncanonical inflammasome pathway can be induced in CECs as well, leading to a further increase in the secretion of active interleukin-1ß over that observed in response to activation of the canonical pathway. In parallel, a more pronounced disruption of tight junctions takes place. We also show that CECs respond to inflammatory stimuli coming from both the apical/blood and the basolateral/brain directions. As a result, CECs can detect factors secreted by pericytes in which the noncanonical inflammasome pathway is activated and respond with inflammatory activation and impairment of the barrier properties. In addition, upon sensing inflammatory signals, CECs release inflammatory factors toward both the blood and the brain sides. Consequently, CECs activate pericytes by upregulating their expression of NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3), an inflammasome-forming pattern recognition receptor. In conclusion, cerebral pericytes and endothelial cells mutually activate each other in inflammation.

Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics.

Peptide-spectrum-match (PSM) scores used in database searching are calibrated to spectrum- or spectrum-peptide-specific null distributions. Some calibration methods rely on specific assumptions and use analytical models (e.g., binomial distributions), whereas other methods utilize exact empirical null distributions. The former may be inaccurate because of unjustified assumptions, while the latter are accurate, albeit computationally exhaustive. Here, we introduce a novel, nonparametric, heuristic PSM score calibration method, called Tailor, which calibrates PSM scores by dividing them with the top 100-quantile of the empirical, spectrum-specific null distributions (i.e., the score with an associated p-value of 0.01 at the tail, hence the name) observed during database searching. Tailor does not require any optimization steps or long calculations; it does not rely on any assumptions on the form of the score distribution (i.e., if it is, e.g., binomial); however, it relies on our empirical observation that the mean and the variance of the null distributions are correlated. In our benchmark, we re-calibrated the match scores of XCorr from Crux, HyperScore scores from X!Tandem, and the p-values from OMSSA with the Tailor method and obtained more spectrum annotations than with raw scores at any false discovery rate level. Moreover, Tailor provided slightly more annotations than E-values of X!Tandem and OMSSA and approached the performance of the computationally exhaustive exact p-value method for XCorr on spectrum data sets containing low-resolution fragmentation information (MS2) around 20-150 times faster. On high-resolution MS2 data sets, the Tailor method with XCorr achieved state-of-the-art performance and produced more annotations than the well-calibrated residue-evidence (Res-ev) score around 50-80 times faster.

Morphotype of bacteroids in different legumes correlates with the number and type of symbiotic NCR peptides.

In legume nodules, rhizobia differentiate into nitrogen-fixing forms called bacteroids, which are enclosed by a plant membrane in an organelle-like structure called the symbiosome. In the Inverted Repeat-Lacking Clade (IRLC) of legumes, this differentiation is terminal due to irreversible loss of cell division ability and is associated with genome amplification and different morphologies of the bacteroids that can be swollen, elongated, spherical, and elongated-branched, depending on the host plant. In Medicago truncatula, this process is orchestrated by nodule-specific cysteine-rich peptides (NCRs) delivered into developing bacteroids. Here, we identified the predicted NCR proteins in 10 legumes representing different subclades of the IRLC with distinct bacteroid morphotypes. Analysis of their expression and predicted sequences establishes correlations between the composition of the NCR family and the morphotypes of bacteroids. Although NCRs have a single origin, their evolution has followed different routes in individual lineages, and enrichment and diversification of cationic peptides has resulted in the ability to impose major morphological changes on the endosymbionts. The wide range of effects provoked by NCRs such as cell enlargement, membrane alterations and permeabilization, and biofilm and vesicle formation is dependent on the amino acid composition and charge of the peptides. These effects are strongly influenced by the rhizobial surface polysaccharides that affect NCR-induced differentiation and survival of rhizobia in nodule cells.

Bias in False Discovery Rate Estimation in Mass-Spectrometry-Based Peptide Identification.

Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an important but often neglected assumption that incorrect spectrum annotations are equally likely to receive either target or decoy peptides. Here we argue that this assumption is often violated in practice, even by popular methods. Preference can be given to target peptides by biased scoring functions, which result in liberal FDR estimations, or to decoy peptides by correlated spectra, which result in conservative estimations.

In Vivo Applicability of Neosartorya fischeri Antifungal Protein 2 (NFAP2) in Treatment of Vulvovaginal Candidiasis.

As a consequence of emerging numbers of vulvovaginitis cases caused by azole-resistant and biofilm-forming Candida species, fast and efficient treatment of this infection has become challenging. The problem is further exacerbated by the severe side effects of azoles as long-term-use medications in the recurrent form. There is therefore an increasing demand for novel and safely applicable effective antifungal therapeutic strategies. The small, cysteine-rich, and cationic antifungal proteins from filamentous ascomycetes are potential candidates, as they inhibit the growth of several Candida spp. in vitro; however, no information is available about their in vivo antifungal potency against yeasts. In the present study, we investigated the possible therapeutic application of one of their representatives in the treatment of vulvovaginal candidiasis, Neosartorya fischeri antifungal protein 2 (NFAP2). NFAP2 inhibited the growth of a fluconazole (FLC)-resistant Candida albicans strain isolated from a vulvovaginal infection, and it was effective against both planktonic cells and biofilm in vitro We observed that the fungal cell-killing activity of NFAP2 is connected to its pore-forming ability in the cell membrane. NFAP2 did not exert cytotoxic effects on primary human keratinocytes and dermal fibroblasts at the MIC in vitro. In vivo murine vulvovaginitis model experiments showed that NFAP2 significantly decreases the number of FLC-resistant C. albicans cells, and combined application with FLC enhances the efficacy. These results suggest that NFAP2 provides a feasible base for the development of a fundamental new, safely applicable mono- or polytherapeutic topical agent for the treatment of superficial candidiasis.

LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

Motivation: Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Results: Here, we present a new convolutional kernel function for protein sequences called the Lempel-Ziv-Welch (LZW)-Kernel. It is based on code words identified with the LZW universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance, which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with Basic Local Alignment Search Tool (BLAST) scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. Availability and implementation: LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. Supplementary information: Supplementary data are available at Bioinformatics Online.