25 papers · ranked by Valyu relevance
Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M. Karlowski
'Wojciech M. Karlowski'] Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for…
Christopher J. Fallaize, Peter Green, Kanti V. Mardia, Stuart Barber
One of the major problems in biology is related to protein folding. The folding process is known to depend on both the protein's sequence (1-D) and structure (3-D). Similarity of both 1-D and 3-D characteristics of different proteins are influenced by the evolutionary distance between the proteins, and need to be…
Hao Xuan, Hongyang Sun, Xiangtao Liu, Hanyuan Zhang + 2 more
Sequence alignment underpins nearly every facet of modern genomics, from genetic testing and cancer profiling to functional genome annotation. Yet, despite decades of algorithmic innovation, most existing aligners remain narrowly optimized for specific tasks, fragmenting analytical workflows and limiting…
K.S Kong, E.Y.K Ng
The work showed that the integrated suite of software tools for detecting criminals using DNA databases has achieved the overall objective by providing a working platform for sequence analysis. The work also demonstrated that by integrating BLAST and FASTA (two widely used and freely available algorithms), plus an…
Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez
The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a…
Suchindra, P. Nagaraj
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many sequencing algorithms developed over the past decades but the sequence alignment using…
Minh Duc Cao, Trevor I Dix, Lloyd Allison
Background Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computationally expensive and unable to deal with low information regions. Furthermore, they lack a…
Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi
Sequences of nucleotides (for DNA and RNA) or aminoacids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in such a way to identify similar regions, to detect evolutionary relationships between…
Veska Gancheva, Hristo Stoev, Clifford J. Steer
Bioinformatics is a rapidly developing field enabling scientific experiments via computer models and simulations. In recent years, there has been an extraordinary growth in biological databases. Therefore, it is extremely important to propose effective methods and algorithms for the fast and accurate processing of…
Orion Penner, Peter Grassberger, Maya Paczuski, Konrad Scheffler
Background Existing sequence alignment algorithms use heuristic scoring schemes based on biological expertise, which cannot be used as objective distance metrics. As a result one relies on crude measures, like the p- or log-det distances, or makes explicit, and often too simplistic, a priori assumptions about sequence…
Petar Arsic, Christoph Mayer
We report a convolutional transformer neural network that is capable of aligning multiple nucleotide sequences. The neural network is based on the U-Net commonly used in image segmentation which we employ to transform unaligned sequences to aligned sequences. For alignment scenarios our Ali-U-Net neural network has…
Ana Arribas‐Gil, Catherine Matias
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 alignments of all the sequences (viewed as paths in a certain space), we construct a…
Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini
'Ramanathan Sowdhamini'] Background Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In…
Anna Paola Muntoni, Andrea Pagnani
DCAlign is a new alignment method able to cope with the conservation and the co-evolution signals that characterize the columns of a multiple sequence alignment of homologous sequences. However, the pre-processing steps required to align a candidate sequence are computationally demanding. We show in v1.0 how to…
Mariana Flores-Torres, Laura Gómez-Romero, Joshua I. Haase-Hernández, Israel Aguilar-Ordóñez + 3 more
In this work, we evaluated several tools used for the alignment of short sequences and found that most aligners execute reasonably well for identical sequences, whereas a variety of alignment errors emerge for dissimilar ones. Since alignments are essential in computational biology, we developed ExtendAlign, a…
David A. Morrison
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 requirements for a solution. The goal of alignment is often stated to be to…
Martin C. Frith
The main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on this idea: find an alignment of two sequence regions, which would be unlikely to exist between unrelated sequences. Unfortunately, it is hard to tell if an…
Amir H Bayegan, Peter Clote
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural homology identification. A number of successful alignment programs…
Amir H. Bayegan, Peter Clote
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural homology identification. A number of successful alignment programs…
Joseph Redshaw, Darren Ting, Alex Brown, Jonathan Hirst + 1 more
Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and timeconsuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating…
Pavel Kohout, Michal Vasina, Marika Majerova, Veronika Novakova + 5 more
Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally…
Arun Shanker, Divya Bhanu, Anjani Alluri, Samriddhi Gupta
The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Acute Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the SARS-CoV-2 has emerged in China. Characterization of spike…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Authors not listed
Sequence is the critical determinant of macromolecular function, yet current polymer design approaches often optimize monomer composition and ratios while ignoring sequence. This creates poorly defined design spaces for active learning that miss the vast combinatorial landscape of sequence possibilities. We introduce…
Authors not listed
Pose prediction of ligands to proteins remains a central challenge of structure-based drug design. Although data leakage and generalizability concerns remain, data-driven methods for pose prediction (i.e. based on deep learning and diffusion) now routinely outperform traditional techniques such as molecular docking. In…