Related papers: Multiple sequence alignment for short sequences
To mitigate the computational complexity in the self-attention mechanism on long sequences, linear attention utilizes computation tricks to achieve linear complexity, while state space models (SSMs) popularize a favorable practice of using…
Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure…
In the multireference alignment model, a signal is observed by the action of a random circular translation and the addition of Gaussian noise. The goal is to recover the signal's orbit by accessing multiple independent observations. Of…
The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction,…
We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising…
Multiple network alignment is the problem of identifying similar and related regions in a given set of networks. While there are a large number of effective techniques for pairwise problems with two networks that scale in terms of edges,…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
Based on the stochastic maximum principle for the partially coupled forward-backward stochastic control system (FBSCS for short), a modified method of successive approximations (MSA for short) is established for stochastic recursive optimal…
We study the problem of efficiently clustering protein sequences in a limited information setting. We assume that we do not know the distances between the sequences in advance, and must query them during the execution of the algorithm. Our…
Maximum-length sequences (m-sequences for short) over finite fields are generated by linear feedback shift registers with primitive characteristic polynomials. These sequences have nice mathematical structures and good randomness properties…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
Millimeter wave (mmWave) communication with large antenna arrays is a promising technique to enable extremely high data rates due to the large available bandwidth in mmWave frequency bands. In addition, given the knowledge of an optimal…
Balancing assembly lines, a family of optimization problems commonly known as Assembly Line Balancing Problem, is notoriously NP-Hard. They comprise a set of problems of enormous practical interest to manufacturing industry due to the…
We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
A framework previously introduced in [3] for solving a sequence of stochastic optimization problems with bounded changes in the minimizers is extended and applied to machine learning problems such as regression and classification. The…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…