Results 81 to 90 of about 1,259,867 (328)

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, Naga Sai Kavya Vaddadi, Ben Langmead   +2 more
doaj   +1 more source

Inverse parametric sequence alignment

Journal of Algorithms, 2002
Summary: We consider the inverse parametric sequence alignment problem, where a sequence alignment, called a reference alignment, is given and the task is to determine parameter values such that the reference alignment is optimal for those parameter values.
Wei Yu, Fangting Sun, David Fernández-Baca   +2 more
openaire   +4 more sources

Photosynthesis under far‐red light—evolutionary adaptations and bioengineering of light‐harvesting complexes

FEBS Letters, EarlyView.
Phototrophs evolved light‐harvesting systems adapted for efficient photon capture in habitats enriched in far‐red radiation. A subset of eukaryotic pigment‐binding proteins can absorb far‐red photons via low‐energy chlorophyll states known as red forms.
Antonello Amelii, Edoardo Andrea Cutolo, Daniele Montepietra, Claudia Battarra, Roberto Caferri, Stefano Capaldi, Zeno Guardini, Luca Dall'Osto, Roberto Bassi   +8 more
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

Vacuolar transport and function of Saccharomyces cerevisiae sterol ester hydrolase Tgl1

FEBS Letters, EarlyView.
Tgl1, one of yeast sterol ester hydrolases, had been found on the lipid droplets where sterol esters are mainly stored. This study revealed that Tgl1 is transported into the vacuole depending on the ESCRT‐I–III complex, and that it exhibits intra‐vacuolar sterol ester hydrolase activity.
Takumi Nakatsuji, Kosuke Shiraishi, Chuqian Wang, Hiroya Yurimoto, Yasuyoshi Sakai, Masahide Oku   +5 more
wiley   +1 more source

An intracellular transporter mitigates the CO2‐induced decline in iron content in Arabidopsis shoots

FEBS Letters, EarlyView.
This study identifies a gene encoding a transmembrane protein, MIC, which contributes to the reduction of shoot Fe content observed in plants under elevated CO2. MIC is a putative Fe transporter localized to the Golgi and endosomal compartments. Its post‐translational regulation in roots may represent a potential target for improving plant nutrition ...
Timothy Mozzanino, Meijie Li, Cécile Fizames, Mattia Adamo, Laurence Lejay, Christian Dubos, Matthieu Platre, Antoine Martin   +7 more
wiley   +1 more source

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV) [PDF]

F1000Research, 2014
The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected
openaire   +3 more sources

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

, 2016
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction.
Drellich, Elizabeth, Gainer-Dewar, Andrew, Harrington, Heather A., He, Qijun, Heitsch, Christine, Poznanović, Svetlana   +5 more
core   +1 more source

A large‐scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression‐free survival

Molecular Oncology, EarlyView.
There is an unmet need in metastatic breast cancer patients to monitor therapy response in real time. In this study, we show how a noninvasive and affordable strategy based on sequencing of plasma samples with longitudinal tracking of tumour fraction paired with a statistical model provides valuable information on treatment response in advance of the ...
Emma J. Beddowes, Mario Ortega Duran, Solon Karapanagiotis, Alistair Martin, Meiling Gao, Riccardo Masina, Ramona Woitek, James Tanner, Fleur Tippin, Justine Kane, Jonathan Lay, Anja Brouwer, Stephen‐John Sammut, Suet‐Feung Chin, Davina Gale, Dana W. Y. Tsui, Sarah‐Jane Dawson, Nitzan Rosenfeld, Maurizio Callari, Oscar M. Rueda, Carlos Caldas   +20 more
wiley   +1 more source

Protein Sequence Alignment Techniques [PDF]

Acta Crystallographica Section D Biological Crystallography, 1998
The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison.
openaire   +4 more sources