Results 11 to 20 of about 3,888,779 (212)

Sequence analysis of the AAA protein family [PDF]

Protein Science, 1997
AbstractThe AAA protein family, a recently recognized group of Walker‐type ATPases, has been subjected to an extensive sequence analysis. Multiple sequence alignments revealed the existence of a region of sequence similarity, the so‐called AAA cassette.
A. Beyer
openaire   +4 more sources

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

Nucleic Acids Research, 2021
Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins.
Zhen Chen, Pei Zhao, Chen Li, Fuyi Li, Dongxu Xiang, Yong-Zi Chen, T. Akutsu, R. Daly, Geoffrey I. Webb, Quan-zhi Zhao, Lukasz Kurgan, Jiangning Song   +11 more
semanticscholar   +1 more source

Representation learning applications in biological sequence analysis

bioRxiv, 2021
Remarkable advances in high-throughput sequencing have resulted in rapid data accumulation, and analyzing biological (DNA/RNA/protein) sequences to discover new insights in biology has become more critical and challenging.
Hitoshi Iuchi, Taro Matsutani, Keisuke Yamada, Natsuki Iwano, Shunsuke Sumi, S. Hosoda, Shitao Zhao, Tsukasa Fukunaga, Michiaki Hamada   +8 more
semanticscholar   +1 more source

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

Current Protocols in Bioinformatics, 2020
The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) provides interactive access to a wide range of the best‐performing bioinformatics tools and databases, including the state‐of‐the‐art protein sequence comparison methods HHblits and HHpred.
Felix Gabler, Seung-Zin Nam, S. Till, M. Mirdita, Martin Steinegger, J. Söding, A. Lupas, V. Alva   +7 more
semanticscholar   +1 more source

ProteinBERT: a universal deep-learning model of protein sequence and function

bioRxiv, 2021
Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis.
N. Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, M. Linial   +4 more
semanticscholar   +1 more source

A clustered set of three Sp-family genes is ancestral in the Metazoa: evidence from sequence analysis, protein domain structure, developmental expression patterns and chromosomal location

BMC Evolutionary Biology, 2010
BackgroundThe Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially ...
Nina D. Schaeper, Nikola-Michael Prpic, E. Wimmer   +2 more
semanticscholar   +1 more source

Designing hardware for protein sequence analysis [PDF]

Bioinformatics, 2003
Abstract We present the architecture of PROSIDIS, a special purpose co-processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Actual tests show speed up figures ranging from 5 to 50 with respect to conventional general-purpose processors.
Marongiu, Alessandro, Palazzari, Paolo, Rosato, Vittorio   +2 more
openaire   +4 more sources

MGnify: the microbiome sequence data analysis resource in 2023

Nucleic Acids Res., 2022
The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences.
Lorna J. Richardson, B. Allen, Germana Baldi, Martin Beracochea, Maxwell L. Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero, G. Cochrane, Lucy J. Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A. Gurbich, Varsha Kale, A. Korobeynikov, Shriya Raj, Alexander B. Rogers, Ekaterina A. Sakharova, Santiago Sanchez, D. Wilkinson, R. Finn   +20 more
semanticscholar   +1 more source

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation

BMC Bioinformatics, 2021
Background The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources.
Elena Tea Russo, Alessandro Laio, Marco Punta   +2 more
doaj   +1 more source

Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining

eLife, 2019
Diabetes is a diverse and complex disease, with considerable variation in phenotypic manifestation and severity. This variation hampers the study of etiological differences and reduces the statistical power of analyses of associations to genetics ...
Isa Kristina Kirk, Christian Simon, Karina Banasik, Peter Christoffer Holm, Amalie Dahl Haue, Peter Bjødstrup Jensen, Lars Juhl Jensen, Cristina Leal Rodríguez, Mette Krogh Pedersen, Robert Eriksson, Henrik Ullits Andersen, Thomas Almdal, Jette Bork-Jensen, Niels Grarup, Knut Borch-Johnsen, Oluf Pedersen, Flemming Pociot, Torben Hansen, Regine Bergholdt, Peter Rossing, Søren Brunak   +20 more
doaj   +1 more source