Results 81 to 90 of about 1,276,854 (326)
Multiple alignment by sequence annealing [PDF]
Bioinformatics, 2007 AbstractMotivation: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time.
Schwartz, Ariel S., Pachter, Lior
openaire +3 more sources
Process-oriented Iterative Multiple Alignment for Medical Process Mining
, 2017 Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality.
Burd, Randall S. +4 more
core +1 more source
Molecular bases of circadian magnesium rhythms across eukaryotes
FEBS Letters, EarlyView.Circadian rhythms in intracellular [Mg2+] exist across eukaryotic kingdoms. Central roles for Mg2+ in metabolism suggest that Mg2+ rhythms could regulate daily cellular energy and metabolism. In this Perspective paper, we propose that ancestral prokaryotic transport proteins could be responsible for mediating Mg2+ rhythms and posit a feedback model ...
Helen K. Feord, Gerben van Ooijen
wiley +1 more source
Global Network Alignment [PDF]
, 2010 Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment.
Natasa Przulj, Oleksii Kuchaiev
core +1 more source
FEBS Letters, EarlyView.This perspective highlights emerging insights into how the circadian transcription factor CLOCK:BMAL1 regulates chromatin architecture, cooperates with other transcription factors, and coordinates enhancer dynamics. We propose an updated framework for how circadian transcription factors operate within dynamic and multifactorial chromatin landscapes ...
Xinyu Y. Nie, Jerome S. Menet
wiley +1 more source
Sequence alignment generation using intermediate sequence search for homology modeling
Computational and Structural Biotechnology Journal, 2020 Protein tertiary structure is important information in various areas of biological research, however, the experimental cost associated with structure determination is high, and computational prediction methods have been developed to facilitate a more ...
Shuichiro Makigaki, Takashi Ishida
doaj +1 more source
Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing
FEBS Letters, EarlyView.Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley +1 more source
Ancestral sequence alignment under optimal conditions
BMC Bioinformatics, 2005 Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs
Brown Daniel G, Hudek Alexander K
doaj +1 more source
Pangenomic genotyping with the marker array
Algorithms for Molecular Biology, 2023 We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array.
Taher Mun +2 more
doaj +1 more source
Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation
FEBS Letters, EarlyView.Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe +3 more
wiley +1 more source