Here we present TM-Aligner, a new tool for transmembrane protein sequence alignment. TM-Aligner is based on Wu-Manber and dynamic string matching algorithm which has significantly improved its accuracy and speed of multiple sequence alignment. We compared TM-Aligner with prevailing other popular ...
Protein Pairwise Sequence Alignment The alignment tools are similar to the DNA alignment tools BLASTP, FASTA Main difference: instead of scoring match (+2) and mismatch (-1) we have similarity scores: Score s(i,j) > 0 if amino acids i and j have similar properties Score s(i,j) is ...
javabioinformaticsgenomicspdbparser-libraryprotein-data-bankprotein-structureprotein-sequencessequence-alignmentprotein-modificationstructure-alignmentstructural-bioinformatics UpdatedAug 9, 2024 Java Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance. ...
MOTIVATION: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS: We describe COBALT, a constraint based alignment tool that im...
Given a superimposed set of two or more protein structures, Match -> Align constructs a corresponding sequence alignment. It does not matter how the input superposition was generated; it could have been created interactively, or with a tool in Chimera such as MatchMaker, or with some other prog...
Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can ...
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 m
Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant ...
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. The......
Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the...