Results 51 to 60 of about 6,883,088 (299)

Cognitively Economical Heuristic for Multiple Sequence Alignment under Uncertainties

Axioms, 2022
This paper introduces a heuristic for multiple sequence alignment aimed at improving real-time object recognition in short video streams with uncertainties.
Milan Gnjatović, Nemanja Maček, Muzafer Saračević, Saša Adamović, Dušan Joksimović, Darjan Karabašević   +5 more
doaj   +1 more source

Design and analysis strategies for robust microbiome ageing research

FEBS Letters, EarlyView.
The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik, İsmail Güderer, Yi Wang, Tayyaba Alvi, Prasoon Pandey, Handan Melike Dönertaş   +5 more
wiley   +1 more source

Benchmarking tools for the alignment of functional noncoding DNA [PDF]

, 2004
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 2004;5(1): 6.Background: Numerous tools have been developed to align genomic sequences.
Celniker SE, Eisen MB, MB Eisen, Stoye J, Bergman CM, Celniker, Susan E., Bergman, Casey M., SE Celniker, Pollard, Daniel A., Pollard DA, CM Bergman, Eisen, Michael B., J Stoye, Stoye, Jens, Stoye, Jens ; https://orcid.org/, DA Pollard   +15 more
core   +5 more sources

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

BMC Bioinformatics, 2010
Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods.
Kryukov Kirill, Saitou Naruya
doaj   +1 more source

Reconstructing enzyme evolution by protein engineering

FEBS Letters, EarlyView.
Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler, Markus R. Busch, Reinhard Sterner   +2 more
wiley   +1 more source

Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences

Algorithms
The standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad, Alibek Kruglikov, Xuhua Xia   +2 more
doaj   +1 more source

Heuristic for Solving the Multiple Alignment Sequence Problem

Revista de Matemática: Teoría y Aplicaciones, 2011
In this paper we developed a new algorithm for solving the problem of multiple sequence alignment (AM S), which is a hybrid metaheuristic based on harmony search and simulated annealing.
Roman Anselmo Mora Gutiérrez, Javier Ramírez Rodriguez, Mayra Elizondo Cortéz   +2 more
doaj   +1 more source

Conserved binding mode but diverse interfaces of MreC‐PBP2 interactions

FEBS Letters, EarlyView.
The crystal structure of abMreC reveals a conserved two β‐barrel architecture and provides structural insights into its role within the bacterial elongasome. The abMreC–abPBP2 complex model identifies the molecular basis of MreC‐mediated PBP2 recognition, contributing to the regulation of peptidoglycan synthesis.
Hyunseok Jang, Hyo Been Jin, Chang Min Kim, So Yeon Lee, Hyun Ho Park   +4 more
wiley   +1 more source

Inferring phylogenies of evolving sequences without multiple sequence alignment [PDF]

, 2014
Alignment-free methods, in which shared properties of sub-sequences (e. g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference.
Bernard, Guillaume, Ragan, Mark A., Poirion, Olivier, Chan, Cheong Xin, Hogan, James M.   +4 more
core   +1 more source

Multiple sequence alignment accuracy and evolutionary distance estimation

BMC Bioinformatics, 2005
Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and ...
Rosenberg Michael S
doaj   +1 more source