Related papers: Aligning biological sequences by exploiting residu…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and…
Social network alignment, aligning different social networks on their common users, is receiving dramatic attention from both academic and industry. All existing studies consider the social network to be static and neglect its inherent…
Deep learning is playing a vital role in every field which involves data. It has emerged as a strong and efficient framework that can be applied to a broad spectrum of complex learning problems which were difficult to solve using…
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…
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…