Related papers: On subset seeds for protein alignment

Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for…

Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…

While DeepMind has tentatively solved protein folding, its inverse problem -- protein design which predicts protein sequences from their 3D structures -- still faces significant challenges. Particularly, the lack of large-scale standardized…

We consider a similarity measure between two sets $A$ and $B$ of vectors, that balances the average and maximum cosine distance between pairs of vectors, one from set $A$ and one from set $B$. As a motivation for this measure, we present…

Supervised (linear) embedding models like Wsabie and PSI have proven successful at ranking, recommendation and annotation tasks. However, despite being scalable to large datasets they do not take full advantage of the extra data due to…

Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…

Sentence embedding methods offer a powerful approach for working with short textual constructs or sequences of words. By representing sentences as dense numerical vectors, many natural language processing (NLP) applications have improved…

Subspace clustering aims to find groups of similar objects (clusters) that exist in lower dimensional subspaces from a high dimensional dataset. It has a wide range of applications, such as analysing high dimensional sensor data or DNA…

Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…

Exact structured inference with neural network scoring functions is computationally challenging but several methods have been proposed for approximating inference. One approach is to perform gradient descent with respect to the output…

With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…

The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…

Network (or Graph) Alignment Algorithms aims to reveal structural similarities among graphs. In particular Local Network Alignment Algorithms (LNAs) finds local regions of similarity among two or more networks. Such algorithms are in…

We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The…

We study the connections between sorting and the binary search tree (BST) model, with an aim towards showing that the fields are connected more deeply than is currently appreciated. While any BST can be used to sort by inserting the keys…

A first step in exploring population structure in crop plants and other organisms is to define the number of subpopulations that exist for a given data set. The genetic marker data sets being generated have become increasingly large over…

Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and structure co-design underexplored. In this paper, we propose…