iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization. [PDF]
Nucleic Acids Res, 2021 Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins.
Chen Z +11 more
europepmc +2 more sources
Word correlation matrices for protein sequence analysis and remote homology detection
BMC Bioinformatics, 2008 Background Classification of protein sequences is a central problem in computational biology. Currently, among computational methods discriminative kernel-based approaches provide the most accurate results.
Meinicke Peter, Lingner Thomas
doaj +2 more sources
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
Proceedings of the National Academy of Sciences of the United States of America, 2004 John E. P. Syka +4 more
openalex +2 more sources
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 +4 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 +7 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 +8 more
semanticscholar +1 more source
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Nature Biotechnology, 2017 VOLUME 35 NUMBER 11 NOVEMBER 2017 NATURE BIOTECHNOLOGY performance was to combine the doublematch criterion with making k-mers as long as possible, which required finding similar and not just exact k-mers. This effectively bases our decision on up to 2 ×
Martin Steinegger, J. Söding
semanticscholar +1 more source
ANTHEPROT: a package for protein sequence analysis using a microcomputer [PDF]
Comput. Appl. Biosci., 1988 Gilbert Deléage +3 more
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STAR Protocols, 2023 Summary: Post-translational modifications (PTMs) serve as key regulatory mechanisms in various cellular processes; altered PTMs can potentially lead to human diseases.
Yu Yan +6 more
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ConSole: using modularity of contact maps to locate solenoid domains in protein structures. [PDF]
, 2014 BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on
Godzik, Adam, Hrabe, Thomas
core +4 more sources