Related papers: Aligning 415 519 proteins in less than two hours o…
Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques employed for increasing…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to…
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…
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…
CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue…
Analyzing the relation between a set of biological sequences can help to identify and understand the evolutionary history of these sequences and the functional relations among them. Multiple Sequence Alignment (MSA) is the main obstacle to…
Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…
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…
Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genomes. Sequence-to-graph alignment is an essential step for the…
Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum clique problems in specific k-partite…
Direct-Coupling Analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from data. In protein families of realistic size, this learning can…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…