Related papers: HSEARCH: fast and accurate protein sequence motif …

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…

This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…

The main objective of the paper is to find the motif information.The functionalities of the proteins are ideally found from their motif information which is extracted using various techniques like clustering with k-means, hybrid k-means,…

Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big…

Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…

Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…

Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…

We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both…

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…

Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…

Detecting repeated variable-length patterns, also called variable-length motifs, has received a great amount of attention in recent years. Current state-of-the-art algorithm utilizes fixed-length motif discovery algorithm as a subroutine to…

Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…

Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained…

Machine learning tasks over image databases often generate masks that annotate image content (e.g., saliency maps, segmentation maps, depth maps) and enable a variety of applications (e.g., determine if a model is learning spurious…

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…

Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…