相关论文: Alignment Metric Accuracy

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…

Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…

Trace alignment algorithms have been used in process mining for discovering the consensus treatment procedures and process deviations. Different alignment algorithms, however, may produce very different results. No widely-adopted method…

The subject of this paper is to study conformance checking for timed models, that is, process models that consider both the sequence of events in a process as well as the timestamps at which each event is recorded. Time-aware process mining…

Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the…

Formal verification provides assurances that a probabilistic system satisfies its specification--conditioned on the system model being aligned with reality. We propose alignment monitoring to watch that this assumption is justified. We…

A distance-based inconsistency indicator, defined by the third author for the consistency-driven pairwise comparisons method, is extended to the incomplete case. The corresponding optimization problem is transformed into an equivalent…

This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…

This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…

Multivariate time series alignment is critical for ensuring coherent analysis across variables, but missing values and timestamp inconsistencies make this task highly challenging. Existing approaches often rely on prior imputation, which…

We introduce a novel method for controlling a motion sequence using an arbitrary temporal control sequence using temporal alignment. Temporal alignment of motion has gained significant attention owing to its applications in motion control…

In this paper, we propose to learn a Mahalanobis distance to perform alignment of multivariate time series. The learning examples for this task are time series for which the true alignment is known. We cast the alignment problem as a…

Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…

Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…

We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by…

The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading…

We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise…

Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…

An overview of current multiple alignment systems to date are described.The useful algorithms, the procedures adopted and their limitations are presented.We also present the quality of the alignments obtained and in which cases(kind of…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…