Sequence Similarity Measures Research Articles

On measuring similarity for sequences of itemsets

Computing the similarity between sequences is a very important challenge for many different data mining tasks. There is a plethora of similarity measures for sequences in the literature, most of them being designed for sequences of items. In this work, we study the problem of measuring the similarity between sequences of itemsets. We focus on the notion of common subsequences as a way to measure similarity between a pair of sequences composed of a list of itemsets. We present new combinatorial results for efficiently counting distinct and common subsequences. These theoretical results are the cornerstone of an effective dynamic programming approach to deal with this problem. In addition, we propose an approximate method to speed up the computation process for long sequences. We have applied our method to various data sets: healthcare trajectories, online handwritten characters and synthetic data. Our results confirm that our measure of similarity produces competitive scores and indicate that our method is relevant for large scale sequential data analysis.

SSM-DENCLUE : Enhanced Approach for Clustering of Sequential Data: Experiments and Test Cases

web usage data is useful to discover interesting patterns related to user traversals, behavior and their characteristics, which helps for the improvement of better Search Engines and Web personalization. Clustering web sessions is to group them based on similarity and consists of minimizing the Intra-cluster similarity and maximizing the Inter-group similarity. The other issue that arises is how to measure similarity between web sessions. There exist multiple similarity measures in the past like Euclidean , Jaccard ,Cosine and many. Most of the similarity measures presented in the history deal only with sequence data but not the order of occurrence of data. A novel similarity measure named SSM(Sequence Similarity Measure) is developed that shows the impact of clustering process ,when both sequence and content information is incorporated while computing similarity between sequences. SSM (Sequence Similarity measure) captures both the order of occurrence of page visits and the page information as well , and compared the results with Euclidean, Jaccard and Cosine similarity measures. Incorporating a new similarity measure, the existing Density clustering technique DENCLUE is enhanced and the new named as SSM-DENCLUE for Web personalization. The Inter-cluster and Intra-cluster distances are computed using Average Levensthien distance (ALD) to demonstrate the usefulness of the proposed approach in the context of web usage mining. This new similarity measure has significant results when comparing similarities between web sessions with other previous measures , and provided good time requirements of the newly developed SSM- DENCLUE algorithms. Experiments are performed on MSNBC.COM website ( free online news channel), in the context of Density based clustering in the domain of Web usage mining.

A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering

Multiple sequence alignment (MSA) is a prominent method for classification of DNA sequences, yet it is hampered with inherent limitations in computational complexity. Alignment-free methods have been developed over past decade for more efficient comparison and classification of DNA sequences than MSA. However, most alignment-free methods may lose structural and functional information of DNA sequences because they are based on feature extractions. Therefore, they may not fully reflect the actual differences among DNA sequences. Alignment-free methods with information conservation are needed for more accurate comparison and classification of DNA sequences. We propose a new alignment-free similarity measure of DNA sequences using the Discrete Fourier Transform (DFT). In this method, we map DNA sequences into four binary indicator sequences and apply DFT to the indicator sequences to transform them into frequency domain. The Euclidean distance of full DFT power spectra of the DNA sequences is used as similarity distance metric. To compare the DFT power spectra of DNA sequences with different lengths, we propose an even scaling method to extend shorter DFT power spectra to equal the longest length of the sequences compared. After the DFT power spectra are evenly scaled, the DNA sequences are compared in the same DFT frequency space dimensionality. We assess the accuracy of the similarity metric in hierarchical clustering using simulated DNA and virus sequences. The results demonstrate that the DFT based method is an effective and accurate measure of DNA sequence similarity.

An alternative approach for clustering web user sessions considering sequential information

Clustering is a prominent technique in data mining applications. It generates groups of data points that are similar to each other in a given aspect. Each group has some inherent latent similarity which is computed using the similarity measures. Clustering web users based on navigational pattern has always been an interesting as well as a challenging task. A web user, based on its navigational pattern, may belong to multiple categories. Intrinsically, web user navigation pattern exhibits sequential property. When dealing with sequence data, a similarity measure should be chosen, which captures both the order as well as content information during computation of similarity among sequences. In this paper, we have utilized the Sequence and Set Similarity Measure S^{3}M with rough set based similarity upper approximation clustering algorithm to group web users based on their navigational patterns. The quality of cluster formed using rough set based clustering algorithm with S^{3}M measure has been compared with the well known clustering algorithm, Density based spatial clustering of applications with noise DBSCAN. The experimental results show the viability of our approach.

Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade

SAR11 is a globally abundant group of Alphaproteobacteria in the oceans that is taxonomically not well defined. It has been suggested SAR11 should be classified into the novel order Pelagibacterales. Features such as conservation of gene content and synteny have been taken as evidence that also the divergent member HIMB59 should be included in the order. However, this proposition is controversial since phylogenetic analyses have questioned the monophyly of this grouping. Here, we performed phylogenetic analyses and reinvestigated the genomic similarity of SAR11 and HIMB59. Our phylogenetic analysis confirmed that HIMB59 is not a sister group to the other SAR11 strains. By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria. First, pairwise sequence similarity measures for the SAR11 and HIMB59 genomes were within the range observed for unrelated pairs of Alphaproteobacteria. Second, pairwise comparisons of gene contents revealed a higher similarity of SAR11 to several other alphaproteobacterial genomes than to HIMB59. Third, the SAR11 genomes are not more similar in gene order to the HIMB59 genome than what they are to several other alphaproteobacterial genomes. Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome. Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

Are we what we do? Exploring group behaviour through user-defined event-sequence similarity

The study of human activity in space and time is an inherent part of human geography. In order to perform such studies, data on the time use of individuals, in terms of sequence and timing of performed activities, are collected and analysed. A common assumption when analysing individuals’ time use is that groups that exhibit similar background and demographic characteristics also display similarities in how they use their time to structure their daily lives. In this article, we set out to investigate the correctness of such assumptions. We propose a visual analytics process based on sequence similarity measures tailored to event-based data such as performed activity sequences. The process allows an analyst to retrieve similarly behaving records according to user-selected similarity preferences and interactively explore aspects of this similarity in a multiple linked-view environment.

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.

BackgroundThe quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult.ResultsWe present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD.ConclusionsConsidering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

A novel hierarchical clustering algorithm for gene sequences

BackgroundClustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. This method transforms DNA sequences into the feature vectors which contain the occurrence, location and order relation of k-tuples in DNA sequence. Afterwards, a hierarchical procedure is applied to clustering DNA sequences based on the feature vectors.ResultsThe proposed distance measure and clustering method are evaluated by clustering functionally related genes and by phylogenetic analysis. This method is also compared with BlastClust, CD-HIT-EST and some others. The experimental results show our method is effective in classifying DNA sequences with similar biological characteristics and in discovering the underlying relationship among the sequences.ConclusionsWe introduced a novel clustering algorithm which is based on a new sequence similarity measure. It is effective in classifying DNA sequences with similar biological characteristics and in discovering the relationship among the sequences.

Querying event sequences by exact match or similarity search: Design and empirical evaluation

Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both.

A Multidimensional Sequence Approach to Measuring Tree Similarity

Tree is one of the most common and well-studied data structures in computer science. Measuring the similarity of such structures is key to analyzing this type of data. However, measuring tree similarity is not trivial due to the inherent complexity of trees and the ensuing large search space. Tree kernel, a state of the art similarity measurement of trees, represents trees as vectors in a feature space and measures similarity in this space. When different features are used, different algorithms are required. Tree edit distance is another widely used similarity measurement of trees. It measures similarity through edit operations needed to transform one tree to another. Without any restrictions on edit operations, the computation cost is too high to be applicable to large volume of data. To improve efficiency of tree edit distance, some approximations were introduced into tree edit distance. However, their effectiveness can be compromised. In this paper, a novel approach to measuring tree similarity is presented. Trees are represented as multidimensional sequences and their similarity is measured on the basis of their sequence representations. Multidimensional sequences have their sequential dimensions and spatial dimensions. We measure the sequential similarity by the all common subsequences sequence similarity measurement or the longest common subsequence measurement, and measure the spatial similarity by dynamic time warping. Then we combine them to give a measure of tree similarity. A brute force algorithm to calculate the similarity will have high computational cost. In the spirit of dynamic programming two efficient algorithms are designed for calculating the similarity, which have quadratic time complexity. The new measurements are evaluated in terms of classification accuracy in two popular classifiers (k-nearest neighbor and support vector machine) and in terms of search effectiveness and efficiency in k-nearest neighbor similarity search, using three different data sets from natural language processing and information retrieval. Experimental results show that the new measurements outperform the benchmark measures consistently and significantly.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Motivation: The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets.Results: We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2.Conclusion: N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences.Availability: The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.htmlContact: goeke@molgen.mpg.de; vingron@molgen.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.

A Novel Similarity Measure for Sequence Data

Abstract —A variety of different metrics has been introduced to measure the similarity of two given sequences. These widely used metrics are ranging from spell correctors and categorizers to new sequence mining applications. Different metrics consider different aspects of sequences, but the essence of any sequence is extracted from the ordering of its elements. In this paper, we propose a novel sequence similarity measure that is based on all ordered pairs of one sequence and where a Hasse diagram is built in the other sequence. In contrast with existing approaches, the idea behind the proposed sequence similarity metric is to extract all ordering features to capture sequence properties. We designed a clustering problem to evaluate our sequence similarity metric. Experimental results showed the superiority of our proposed sequence similarity metric in maximizing the purity of clustering compared to metrics such as d2, Smith-Waterman, Levenshtein, and Needleman-Wunsch. The limitation of those methods originates from some neglected sequence features, which are considered in our proposed sequence similarity metric.

Efficient bitmap-based indexing of time-based interval sequences

In this paper, we discuss similarity searches for time series data represented as interval sequences. For instance, the time series of phone call records can be represented by time-based interval sequences, or T-interval sequences, which consist of the start and end times of the call records. To support an efficient similarity search for such sequences, we address the desirable semantics for similarity measures for the T-interval sequences, observe how existing measures fail to address such semantics, and propose a new measure that satisfies all our semantics. We then propose approximate encoding methods for T-interval sequences. More specifically, we propose two bitmap-based feature extraction methods: (1) a bin-bitmap encoding method that transforms the T-interval sequences into bitmaps of fixed length, and (2) a segmented feature extraction method that takes the longest bitmap sequences of consecutive ‘1’ elements. Finally, we propose two query processing schemes using these bitmap-based approximate representations. We validate the efficiency and effectiveness of our proposed solutions empirically.

Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length

The D(2) statistic, defined as the number of matches of words of some pre-specified length k, is a computationally fast alignment-free measure of biological sequence similarity. However there is some debate about its suitability for this purpose as the variability in D(2) may be dominated by the terms that reflect the noise in each of the single sequences only. We examine the extent of the problem and the effectiveness of overcoming it by using two mean-centred variants of this statistic, D(2)* and D(2c). We conclude that all three statistics are potentially useful measures of sequence similarity, for which reasonably accurate p-values can be estimated under a null hypothesis of sequences composed of identically and independently distributed letters. We show that D(2) and D(2)c, and to a somewhat lesser extent D(2)*, perform well in tests to classify moderate length query sequences as putative cis-regulatory modules.

State-space dynamics distance for clustering sequential data

This paper proposes a novel similarity measure for clustering sequential data. We first construct a common state space by training a single probabilistic model with all the sequences in order to get a unified representation for the dataset. Then, distances are obtained attending to the transition matrices induced by each sequence in that state space. This approach solves some of the usual overfitting and scalability issues of the existing semi-parametric techniques that rely on training a model for each sequence. Empirical studies on both synthetic and real-world datasets illustrate the advantages of the proposed similarity measure for clustering sequences.

A New Similarity Metric for Sequential Data

In many data mining applications, both classification and clustering algorithms require a distance/similarity measure. The central problem in similarity based clustering/classification comprising sequential data is deciding an appropriate similarity metric. The existing metrics like Euclidean, Jaccard, Cosine, and so forth do not exploit the sequential nature of data explicitly. In this paper, the authors propose a similarity preserving function called Sequence and Set Similarity Measure (S3M) that captures both the order of occurrence of items in sequences and the constituent items of sequences. The authors demonstrate the usefulness of the proposed measure for classification and clustering tasks. Experiments were conducted on benchmark datasets, that is, DARPA’98 and msnbc, for classification task in intrusion detection and clustering task in web mining domains. Results show the usefulness of the proposed measure.

Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences

Classifying proteins into subgroups with similar molecular function on the basis of sequence is an important step in deriving reliable functional annotations computationally. So far, however, available classification procedures have been evaluated against protein subgroups that are defined by experts using mainly qualitative descriptions of molecular function. Recently, in vitro DNA-binding preferences to all possible 8-nt DNA sequences have been measured for 178 mouse homeodomains using protein-binding microarrays, offering the unprecedented opportunity of evaluating the classification methods against quantitative measures of molecular function. To this end, we automatically derive homeodomain subtypes from the DNA-binding data and independently group the same domains using sequence information alone. We test five sequence-based methods, which use different sequence-similarity measures and algorithms to group sequences. Results show that methods that optimize the classification robustness reflect well the detailed functional specificity revealed by the experimental data. In some of these classifications, 73–83% of the subfamilies exactly correspond to, or are completely contained in, the function-based subtypes. Our findings demonstrate that certain sequence-based classifications are capable of yielding very specific molecular function annotations. The availability of quantitative descriptions of molecular function, such as DNA-binding data, will be a key factor in exploiting this potential in the future.

Using Local Alignments for Relation Recognition

This paper discusses the problem of marrying structural similarity with semantic relatedness for Information Extraction from text. Aiming at accurate recognition of relations, we introduce local alignment kernels and explore various possibilities of using them for this task. We give a definition of a local alignment (LA) kernel based on the Smith-Waterman score as a sequence similarity measure and proceed with a range of possibilities for computing similarity between elements of sequences. We show how distributional similarity measures obtained from unlabeled data can be incorporated into the learning task as semantic knowledge. Our experiments suggest that the LA kernel yields promising results on various biomedical corpora outperforming two baselines by a large margin. Additional series of experiments have been conducted on the data sets of seven general relation types, where the performance of the LA kernel is comparable to the current state-of-the-art results.

A visual framework for sequence analysis using n-grams and spectral rearrangement

Protein sequences are often composed of regions that have distinct evolutionary histories as a consequence of domain shuffling, recombination or gene conversion. New approaches are required to discover, visualize and analyze these sequence regions and thus enable a better understanding of protein evolution. Here, we have developed an alignment-free and visual approach to analyze sequence relationships. We use the number of shared n-grams between sequences as a measure of sequence similarity and rearrange the resulting affinity matrix applying a spectral technique. Heat maps of the affinity matrix are employed to identify and visualize clusters of related sequences or outliers, while n-gram-based dot plots and conservation profiles allow detailed analysis of similarities among selected sequences. Using this approach, we have identified signatures of domain shuffling in an otherwise poorly characterized family, and homology clusters in another. We conclude that this approach may be generally useful as a framework to analyze related, but highly divergent protein sequences. It is particularly useful as a fast method to study sequence relationships prior to much more time-consuming multiple sequence alignment and phylogenetic analysis. A software implementation (MOSAIC) of the framework described here can be downloaded from http://bioinformatics.org.au/mosaic/ m.ragan@uq.edu.au Supplementary data are available at Bioinformatics online.

V3 Loop Sequence Space Analysis Suggests Different Evolutionary Patterns of CCR5- and CXCR4-Tropic HIV

The V3 loop of human immunodeficiency virus type 1 (HIV-1) is critical for coreceptor binding and is the main determinant of which of the cellular coreceptors, CCR5 or CXCR4, the virus uses for cell entry. The aim of this study is to provide a large-scale data driven analysis of HIV-1 coreceptor usage with respect to the V3 loop evolution and to characterize CCR5- and CXCR4-tropic viral phenotypes previously studied in small- and medium-scale settings. We use different sequence similarity measures, phylogenetic and clustering methods in order to analyze the distribution in sequence space of roughly 1000 V3 loop sequences and their tropism phenotypes. This analysis affords a means of characterizing those sequences that are misclassified by several sequence-based coreceptor prediction methods, as well as predicting the coreceptor using the location of the sequence in sequence space and of relating this location to the CD4+ T-cell count of the patient. We support previous findings that the usage of CCR5 is correlated with relatively high sequence conservation whereas CXCR4-tropic viruses spread over larger regions in sequence space. The incorrectly predicted sequences are mostly located in regions in which their phenotype represents the minority or in close vicinity of regions dominated by the opposite phenotype. Nevertheless, the location of the sequence in sequence space can be used to improve the accuracy of the prediction of the coreceptor usage. Sequences from patients with high CD4+ T-cell counts are relatively highly conserved as compared to those of immunosuppressed patients. Our study thus supports hypotheses of an association of immune system depletion with an increase in V3 loop sequence variability and with the escape of the viral sequence to distant parts of the sequence space.