Sequence Similarity Measures Research Articles

Graph-based analysis of DNA sequence comparison in closed cotton species: A generalized method to unveil genetic connections.

Graph theory provides a systematic method for modeling and analysing complicated biological data as an effective bioinformatics tool. Based on current trends, the number of DNA sequences in the DNA database is growing quickly. To determine the origin of a species and identify homologous sequences, it is crucial to detect similarities in DNA sequences. Alignment-free techniques are required for accurate measures of sequence similarity, which has been one of the main issues facing computational biologists. The current study provides a mathematical technique for comparing DNA sequences that are constructed in graph theory. The sequences of each DNA were divided into pairs of nucleotides, from which weighted loop digraphs and corresponding weighted vectors were computed. To check the sequence similarity, distance measures like Cosine, Correlation, and Jaccard were employed. To verify the method, DNA segments from the genomes of ten species of cotton were tested. Furthermore, to evaluate the efficacy of the proposed methodology, a K-means clustering method was performed. This study proposes a proof-of-model that utilises a distance matrix approach that promises impressive outcomes with future optimisations to be made to the suggested solution to get the hundred percent accurate result. In the realm of bioinformatics, this paper highlights the use of graph theory as an effective tool for biological data study and sequence comparison. It's expected that further optimization in the proposed solution can bring remarkable results, as this paper presents a proof-of-concept implementation for a given set of data using the proposed distance matrix technique.

Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications.

Antibodies are proteins produced by our immune system that have been harnessed as biotherapeutics. The discovery of antibody-based therapeutics relies on analyzing large volumes of diverse sequences coming from phage display or animal immunizations. Identification of suitable therapeutic candidates is achieved by grouping the sequences by their similarity and subsequent selection of a diverse set of antibodies for further tests. Such groupings are typically created using sequence-similarity measures alone. Maximizing diversity in selected candidates is crucial to reducing the number of tests of molecules with near-identical properties. With the advances in structural modeling and machine learning, antibodies can now be grouped across other diversity dimensions, such as predicted paratopes or three-dimensional structures. Here we benchmarked antibody grouping methods using clonotype, sequence, paratope prediction, structure prediction, and embedding information. The results were benchmarked on two tasks: binder detection and epitope mapping. We demonstrate that on binder detection no method appears to outperform the others, while on epitope mapping, clonotype, paratope, and embedding clusterings are top performers. Most importantly, all the methods propose orthogonal groupings, offering more diverse pools of candidates when using multiple methods than any single method alone. To facilitate exploring the diversity of antibodies using different methods, we have created an online tool-CLAP-available at (clap.naturalantibody.com) that allows users to group, contrast, and visualize antibodies using the different grouping methods.

Systematic evaluation of B-cell clonal family inference approaches

The reconstruction of clonal families (CFs) in B-cell receptor (BCR) repertoire analysis is a crucial step to understand the adaptive immune system and how it responds to antigens. The BCR repertoire of an individual is formed throughout life and is diverse due to several factors such as gene recombination and somatic hypermutation. The use of Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using next generation sequencing enabled the generation of full BCR repertoires that also include rare CFs. The reconstruction of CFs from AIRR-seq data is challenging and several approaches have been developed to solve this problem. Currently, most methods use the heavy chain (HC) only, as it is more variable than the light chain (LC). CF reconstruction options include the definition of appropriate sequence similarity measures, the use of shared mutations among sequences, and the possibility of reconstruction without preliminary clustering based on V- and J-gene annotation. In this study, we aimed to systematically evaluate different approaches for CF reconstruction and to determine their impact on various outcome measures such as the number of CFs derived, the size of the CFs, and the accuracy of the reconstruction. The methods were compared to each other and to a method that groups sequences based on identical junction sequences and another method that only determines subclones. We found that after accounting for data set variability, in particular sequencing depth and mutation load, the reconstruction approach has an impact on part of the outcome measures, including the number of CFs. Simulations indicate that unique junctions and subclones should not be used as substitutes for CF and that more complex methods do not outperform simpler methods. Also, we conclude that different approaches differ in their ability to correctly reconstruct CFs when not considering the LC and to identify shared CFs. The results showed the effect of different approaches on the reconstruction of CFs and highlighted the importance of choosing an appropriate method.

Scalable neighbour search and alignment with uvaia.

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.

A Novel Similarity Measure of Spatiotemporal Event Setting Sequences: Method Development and Case Study

Examining the similarity of event environments or surroundings—more precisely, settings—provides additional insight in analyzing event sequences, as it provides information about the context and potential common factors that may have influenced them. This article proposes a new similarity measure for event setting sequences, which involve the space and time in which events occur. While similarity measures for spatiotemporal event sequences have been studied, the settings and setting sequences have not yet been studied. While modeling event setting sequences, we consider spatial and temporal scales to define the bounds of the setting and incorporate dynamic variables alongside static variables. Using a matrix-based representation and an extended Jaccard index, we developed new similarity measures that allow for the use of all variable data types. We successfully used these similarity measures coupled with other multivariate statistical analysis approaches in a case study involving setting sequences and pollution event sequences associated with the same monitoring stations, which validate the hypothesis that more similar spatial-temporal settings or setting sequences may generate more similar events or event sequences. In conclusion, the developed similarity measures have wide application beyond the case study to other disciplinary contexts and geographical settings. They offer researchers a powerful tool for understanding different factors and their dynamics corresponding to occurrences of spatiotemporal event sequences.

An adaptive HMM method to simulate and forecast ocean chemistry data in aquaculture

Due to the multifaceted influences of many factors and complex mechanisms, accurate predictions of ocean chemistry data are difficult to achieve. To address this problem, this paper proposes an adaptive hidden Markov model (AHMM) for predicting ocean chemistry data from aquaculture farms in eastern China. The periodic, trend and residual terms of the original sequence are obtained through Seasonal and Trend decomposition using Loess (STL), which effectively reveals the variation trend of the sequence. For the period and trend terms of the sequence, the autonomous search grasshopper optimization algorithm (ASGOA) is employed to train the parameters of the HMM, which avoids the problems of easily falling into local optima and the dependence on the initial value in the parameter training process. To predict ocean chemistry data, a sequence similarity measurement method is proposed to match similar sequences in the historical interval, and a linear regression equation is constructed for sequence similarity and the difference between the predicted value and the value at the previous time based on the HMM. The results have revealed that the MAE value decreases by 25.5%, MSE value by 45.9%, RMSE value by 27.4%, MAPE value by 39.5% and R2 increases by 6%. Compared with other prediction algorithms under the same conditions, the prediction method proposed in this paper is easily understandable and manages to achieve better prediction performance. This work can serve as a reference for predicting other ocean chemistry data and for the sustainable management of aquaculture ecosystems.

Context-Aware Practice Problem Recommendation Using Learners’ Skill Level Navigation Patterns

The use of programming online judges (POJs) has risen dramatically in recent years, owing to the fact that the auto-evaluation of codes during practice motivates students to learn programming. Since POJs have greater number of programming problems in their repository, learners experience information overload. Recommender systems are a common solution to information overload. Current recommender systems used in e-learning platforms are inadequate for POJ since recommendations should consider learners’ current context, like learning goals and current skill level (topic knowledge and difficulty level). To overcome the issue, we propose a context-aware practice problem recommender system based on learners’ skill level navigation patterns. Our system initially performs skill level navigation pattern mining to discover frequent skill level navigations in the POJ and to find learners’ learning goals. Collaborative filtering (CF) and content-based filtering approaches are employed to recommend problems in the current and next skill levels based on frequent skill level navigation patterns. The sequence similarity measure is used to find the top k neighbors based on the sequence of problems solved by the learners. The experiment results based on the real-world POJ dataset show that our approach considering the learners’ current skill level and learning goals outperforms the other approaches in practice problem recommender systems.

A fast and efficient algorithm for DNA sequence similarity identification

DNA sequence similarity analysis is necessary for enormous purposes including genome analysis, extracting biological information, finding the evolutionary relationship of species. There are two types of sequence analysis which are alignment-based (AB) and alignment-free (AF). AB is effective for small homologous sequences but becomes NP-hard problem for long sequences. However, AF algorithms can solve the major limitations of AB. But most of the existing AF methods show high time complexity and memory consumption, less precision, and less performance on benchmark datasets. To minimize these limitations, we develop an AF algorithm using a 2D k-mer count matrix inspired by the CGR approach. Then we shrink the matrix by analyzing the neighbors and then measure similarities using the best combinations of pairwise distance (PD) and phylogenetic tree methods. We also dynamically choose the value of k for k-mer. We develop an efficient system for finding the positions of k-mer in the count matrix. We apply our system in six different datasets. We achieve the top rank for two benchmark datasets from AFproject, 100% accuracy for two datasets (16 S Ribosomal, 18 Eutherian), and achieve a milestone for time complexity and memory consumption in comparison to the existing study datasets (HEV, HIV-1). Therefore, the comparative results of the benchmark datasets and existing studies demonstrate that our method is highly effective, efficient, and accurate. Thus, our method can be used with the top level of authenticity for DNA sequence similarity measurement.

Phage-bacterial contig association prediction with a convolutional neural network.

MotivationPhage–host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on various sequence similarity measures or machine learning approaches. These are often based on whole viral and host genomes, but in metagenomics-based studies, we rarely have whole genomes but rather must rely on contigs that are sometimes as short as hundreds of bp long. Therefore, we need programs that predict hosts of phage contigs on the basis of these short contigs. Although most existing programs can be applied to metagenomic datasets for these predictions, their accuracies are generally low. Here, we develop ContigNet, a convolutional neural network-based model capable of predicting phage–host matches based on relatively short contigs, and compare it to previously published VirHostMatcher (VHM) and WIsH.ResultsOn the validation set, ContigNet achieves 72–85% area under the receiver operating characteristic curve (AUROC) scores, compared to the maximum of 68% by VHM or WIsH for contigs of lengths between 200 bps to 50 kbps. We also apply the model to the Metagenomic Gut Virus (MGV) catalogue, a dataset containing a wide range of draft genomes from metagenomic samples and achieve 60–70% AUROC scores compared to that of VHM and WIsH of 52%. Surprisingly, ContigNet can also be used to predict plasmid-host contig associations with high accuracy, indicating a similar genetic exchange between mobile genetic elements and their hosts.Availability and implementationThe source code of ContigNet and related datasets can be downloaded from https://github.com/tianqitang1/ContigNet.

New Method for Sequence Similarity Analysis Based on the Position and Frequency of Statistically Significant Repeats

Background: The analysis of DNA nucleotide sequence similarity among different species is crucial in identifying their functional, structural or evolutionary relationships. The number of bioinformatics tools designed to perform the similarity analysis of nucleotide sequences has been growing rapidly. According to the current literature, alignment-free methods have not been performed on repetitive nucleotide sequence of different lengths. Objective: To develop a new algorithm for determining sequence characteristics and similarity based on statistically significant repetitive elements of different lengths, which are located in analyzed sequences. Methods: This paper presents Repeats-Position/Frequency method (R-P/F method), for determining nucleotide sequence similarity which takes into consideration statistically significant repetitive parts of analyzed sequences. It is based on information theory and the fact that both position and frequency of repeated sequences are not expected to occur with the identical presence in a random sequence of the same length. Nucleotide sequences are presented in rn-dimensional vector space and their hierarchy is constructed by applying hierarchical clustering algorithm. Results: R-P/F method has been validated on multiple data sets of nucleotide sequences and compared with results obtained from alignment-based algorithms BLAST and Clustal Omega, and multiple wellestablished alignment-free dissimilarity measures. Presented method provides results comparable with other commonly used methods focused on resolving the same problem, with the novel view on the used repetitive parts of sequences in these calculations. Conclusion: The presented, novel algorithm for calculating sequence similarity measure is effective in discovering relationships among the sequences and makes a powerful and complementary addition to existing sequence similarity methods.

K-mer Content Changes with Node Degree in Promoter-Enhancer Network of Mouse ES Cells.

Maps of Hi-C contacts between promoters and enhancers can be analyzed as networks, with cis-regulatory regions as nodes and their interactions as edges. We checked if in the published promoter–enhancer network of mouse embryonic stem (ES) cells the differences in the node type (promoter or enhancer) and the node degree (number of regions interacting with a given promoter or enhancer) are reflected by sequence composition or sequence similarity of the interacting nodes. We used counts of all k-mers (k = 4) to analyze the sequence composition and the Euclidean distance between the k-mer count vectors (k-mer distance) as the measure of sequence (dis)similarity. The results we obtained with 4-mers are interpretable in terms of dinucleotides. Promoters are GC-rich as compared to enhancers, which is known. Enhancers are enriched in scaffold/matrix attachment regions (S/MARs) patterns and depleted of CpGs. Furthermore, we show that promoters are more similar to their interacting enhancers than vice-versa. Most notably, in both promoters and enhancers, the GC content and the CpG count increase with the node degree. As a consequence, enhancers of higher node degree become more similar to promoters, whereas higher degree promoters become less similar to enhancers. We confirmed the key results also for human keratinocytes.

Secure and Usable Handshake Based Pairing for Wrist-Worn Smart Devices on Different Users

Wrist-worn smart devices are being used to share various sensitive personal information in various fields such as social, medical treatment, sports, etc. Secure pairing establishing a trusted channel between involved devices is a prerequisite to ensure data transmission security. Handshake has been employed to realize secure pairing between devices worn by different users without pre-shared knowledge, the participation of third parties or complicated user interactions. However, existing schemes cannot meet the practical requirement in terms of time delay and security. In this paper, we present a secure and usable pairing scheme utilizing the handshake acceleration data. Specifically, we propose an optimal feature selection algorithm based on Euclidean distance sorting which improves the success rate and security of the system. In addition, we use Pearson correlation coefficient based feature sequence similarity measurement approach to enhance the accuracy of pairing scheme. Theoretical and experimental security analysis indicates that our solution can resist active and passive attacks. What’s more, the experimental results demonstrate that the proposed solution has a high key generation rate of 87 bits per second, and completes security pairing in less than 4 s.

Discovering Travel Spatiotemporal Pattern Based on Sequential Events Similarity

Travel route preferences can strongly interact with the events that happened in networked traveling, and this coevolving phenomena are essential in providing theoretical foundations for travel route recommendation and predicting collective behaviour in social systems. While most literature puts the focus on route recommendation of individual scenic spots instead of city travel, we propose a novel approach named City Travel Route Recommendation based on Sequential Events Similarity (CTRR-SES) by applying the coevolving spreading dynamics of the city tour networks and mine the travel spatiotemporal patterns in the networks. First, we present the Event Sequence Similarity Measurement Method based on modelling tourists’ travel sequences. The method can help measure similarities in various city travel routes, which combine different scenic types, time slots, and relative locations. Second, by applying the user preference learning method based on scenic type, we learn from the user’s city travel historical data and compute the personalized travel preference. Finally, we verify our algorithm by collecting data of 54 city travellers of their historical spatiotemporal routes in the ten most popular cities from Mafeng.com. CTRR-SES shows better performance in predicting the user’s new city travel sequence fitting the user’s individual preference.

An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction

BackgroundAlignment-free methods for sequence comparisons have become popular in many bioinformatics applications, specifically in the estimation of sequence similarity measures to construct phylogenetic trees. Recently, the average common substring measure, ACS, and its k-mismatch counterpart, ACSk, have been shown to produce results as effective as multiple-sequence alignment based methods for reconstruction of phylogeny trees. Since computing ACSk takes O(n logkn) time and hence impractical for large datasets, multiple heuristics that can approximate ACSk have been introduced.ResultsIn this paper, we present a novel linear-time heuristic to approximate ACSk, which is faster than computing the exact ACSk while being closer to the exact ACSk values compared to previously published linear-time greedy heuristics. Using four real datasets, containing both DNA and protein sequences, we evaluate our algorithm in terms of accuracy, runtime and demonstrate its applicability for phylogeny reconstruction. Our algorithm provides better accuracy than previously published heuristic methods, while being comparable in its applications to phylogeny reconstruction.ConclusionsOur method produces a better approximation for ACSk and is applicable for the alignment-free comparison of biological sequences at highly competitive speed. The algorithm is implemented in Rust programming language and the source code is available at https://github.com/srirampc/adyar-rs.

Investigating the Changes in Amino Acid Properties in the Evolutionary and Multi-Scale Context

Understanding protein mutations is critical for comprehending evolution, drug development, personalized medicine, genomics and much more throughout biology. Classification here is performed by using features, which can be generated/extracted from data, or chosen by an investigator. One kind of feature set showing initial promise not only for classification but also finding out what the basis is for each classification utilizes the physical properties of amino acids. It has been shown that there are periodicities and patterns in protein sequences when they are encoded as these physical property values. An encoding of a sequence where each residue becomes a vector of the amino acid's physical property values provides much more information for sequence similarity measures and can serve as feature components for classifiers. Once a classifier is constructed and trained, it can then be analyzed for feature importance. One of the best methods for this is the permutation importance algorithm. For each of the features, the values are randomly permuted, and then the prediction error is recalculated. The change in the error determines the feature's importance for any specific model, and this technique can be used on any trained classification or regression model. Classification of protein mutants based on physical properties combined with permutation importance can reveal information about why or how each mutation leads to changes in structure, dynamics or function. Extensions include investigating the correlations between properties at residues seen to be correlated in the sequence alignments. This method can be used on any scale, with any set of features, making it a potentially powerful tool for protein analysis.

Pioneering Methods for Enhancing PPI and Phenotype Networks for Candidate Disease Prioritization

The physical contacts of high-specificity between two or more protein molecules constitute Protein-Protein Interactions (PPIs). PPI networks are modeled through graphs where node denotes proteins and edges denote interaction between proteins. The PPI network plays an important role to identify the interesting disease gene candidates. But, the PPI network usually contains false interactions. Many techniques have been proposed to reconstruct PPI network to remove false interactions and improve ranking of candidate disease. Random Walk with Restart on Diffusion profile (RWRDP) and Random Walk on a Reliable Heterogeneous Network (RWRHN) was two among them. In these methods, Gene topological similarity was incorporated with original PPI network to reconstruct new PPI network. Phenotype network was constructed by calculating similarity between gene phenotypes. The reconstructed network and phenotype networks were combined to rank candidate disease genes. However, the PPI reconstruction was fully related with the quality of protein interaction data. In order to enhance the reconstruction of PPI, a Piecewise Linear Regression (PLR) based protein sequence similarity measure and Bat Algorithm based gene expression similarity were proposed with RHN. In this paper, additional measure called Interaction Level Sub cellular Localization Score (ILSLS) is proposed to further reduce the false interaction in the reconstruction of PPI network. ILSLS is the combination of Normalized Sub cellular Localization score (NSL) and Protein Multiple Location Prediction score (PMLP). The proposed work is named as Random Walker on Optimized Trustworthy Heterogeneous Sub Cellular localization aware Network (RW-OTHSN). In order to enhance the ranking of RW-OTHSN, phenotype structure is considered while construction phenotype network to rank the candidate disease genes. The phenotype structure is characterized based on h*-sequence model which identify highly discriminative signatures with only a small number of genes. This proposed work is named as Random Walker on Optimized Trustworthy Heterogeneous Sub Cellular localization and Phenotype structure aware Network (RW-OTHSPN). The efficiency of the proposed methods are evaluated on PPI network database in terms of Average degree, Relative Frequency for PPI reconstruction, Number of successful predictions, precision and recall for candidate disease gene ranking.

A review of alignment based similarity measures for web usage mining

In order to understand web-based application user behavior, web usage mining applies unsupervised learning techniques to discover hidden patterns from web data that captures user browsing on web sites. For this purpose, web session clustering has been among the most popular approaches to group users with similar browsing patterns that reflect their common interest. An adequate web session clustering implementation significantly depends on the measure that is used to evaluate the similarity of sessions. An efficient approach to evaluate session similarity is sequence alignment, which is known as the task of determining the similarity of elements between sequences. In this paper, we review and compare sequence alignment-based measures for web sessions, and also discuss sequence similarity measures that are not alignment-based. This review also provides a perspective of sequence similarity measures that manipulate web sessions in usage clustering process.

Ultrasonic echo processing method based on dual-Gaussian attenuation model

Ultrasonic non-destructive testing, which is one of the most important and rapidly developed non-destructive testing technologies, is widely used in industrial production and other areas. Signal de-noising and feature extraction, whose performance directly affects the evaluation of non-destructive testing results, are the key technologies of ultrasonic non-destructive testing data processing, and also the core elements of ultrasonic non-destructive testing. Therefore, the research on them has important academic significance and practical value. In order to solve the problem of parameter estimation and noise reduction of ultrasonic echo in strong noise background, a novel ultrasonic echo processing method is proposed in this paper. The principle of the proposed method in this paper is as follows. The ultrasonic echo, which is generated by modulating the ultrasonic transducer, has a specific structure, but the noise in practical engineering is usually a Gauss random process, therefore the noise is independent of the ultrasonic signal structure. In this paper, the problem of parameter estimation and noise reduction of ultrasonic echo signal are converted into a function optimization problem by establishing the model of ultrasonic signal, determining the objective function, optimizing the objective function, estimating the parameters, and reconstructing the ultrasonic signal. Firstly, a dual gaussian attenuation mathematical model of ultrasonic signal is established based on practical engineering experience. Secondly, the cosine similarity function, an effective measure of data sequence similarity, is selected as an objective function according to the observed echo and the established ultrasonic signal model. Thirdly, the artificial bee colony algorithm is selected to optimize the objective function to obtain the optimal estimation parameters of the ultrasonic signal from the noisy ultrasonic echo. Fourthly, the estimation of de-noising ultrasonic signal is reconstructed by the optimal parameters based on the established ultrasonic signal mathematical model. The processing results of simulated ultrasonic echoes and measured ultrasonic echoes show that the proposed method can accurately estimate the parameters of ultrasonic signal from strong background noise whose signal-to-noise ratio is lowest, as low as –10 dB. In addition, compared with the adaptive threshold based wavelet method and empirical mode decomposition method, the proposed method in this paper shows the good de-noising performance. Furthermore, compared with the commonly used exponential model and Gaussian model in numerical and simulation analysis, the proposed dual gaussian attenuation mathematical model of ultrasonic signal in this paper can well simulate the measured ultrasonic signal, with a mean square error of 9.4 × 10<sup>–5</sup> and normalized correlation coefficient of 0.98.

Detecting life signatures with RNA sequence similarity measures

The RNA World is currently the most plausible hypothesis for explaining the origins of life on Earth. The supporting body of evidence is growing and it comes from multiple areas, including astrobiology, chemistry, biology, mathematics, and, in particular, from computer simulations. Such methods frequently assume the existence of a hypothetical species on Earth, around three billion years ago, with a base sequence probably dissimilar from any in known genomes. However, it is often hard to verify whether or not a hypothetical sequence has the characteristics of biological sequences, and is thus likely to be functional. The primary objective of the presented research was to verify the possibility of building a computational ‘life probe’ for determining whether a given genetic sequence is biological, and assessing the sensitivity of such probes to the signatures of life present in known biological sequences. We have proposed decision algorithms based on the normalized compression distance (NCD) and Levenshtein distance (LD). We have validated the proposed method in the context of the RNA World hypothesis using short genetic sequences shorter than the error threshold value (i.e., 100 nucleotides). We have demonstrated that both measures can be successfully used to construct life probes that are significantly better than a random decision procedure, while varying from each other when it comes to detailed characteristics. We also observed that fragments of sequences related to replication have better discriminatory power than sequences having other molecular functions. In a broader context, this shows that the signatures of life in short RNA samples can be effectively detected using relatively simple means.

Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.

Word-based or ‘alignment-free’ sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Here, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM.