Extended many-item similarity indices for sets of nucleotide and protein sequences
Computational and Structural Biotechnology Journal, 2021 Quantification of similarities between protein sequences or DNA/RNA strands is a (sub-)task that is ubiquitously present in bioinformatics workflows, and is usually accomplished by pairwise comparisons of sequences, utilizing simple (e.g.
Dávid Bajusz +3 more
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Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences. [PDF]
PLoS ONE, 2015 Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences.
Kun Tian +5 more
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More-SPEED: Enhancing Protein Activity Prediction from DNA Sequences
Iraqi Journal for Computer Science and Mathematics, 2023 This work presents More-SPEED, a novel model for accurately predicting protein activity while minimizing computational demands. Leveraging optimized structures and data preprocessing techniques, More-SPEED achieves high accuracy in protein activity ...
Samaher Al-Janabi, Zena A. Kadhuim
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Predicting target DNA sequences of DNA-binding proteins based on unbound structures. [PDF]
PLoS ONE, 2012 DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions.
Chien-Yu Chen +5 more
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A linear model for transcription factor binding affinity prediction in protein binding microarrays. [PDF]
PLoS ONE, 2011 Protein binding microarrays (PBM) are a high throughput technology used to characterize protein-DNA binding. The arrays measure a protein's affinity toward thousands of double-stranded DNA sequences at once, producing a comprehensive binding specificity ...
Matti Annala +3 more
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A Novel Image Cryptosystem Inspired by the Generation of Biological Protein Sequences
IEEE Access, 2023 Image encryption is essential to keep images secure either in personal devices or over the cloud drives. Various robust image cryptosystems have been implemented during the past decades to keep the encrypted images far from illegal decryption by ...
Mohammad Nassef +2 more
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Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2. [PDF]
PLoS ONE, 2011 BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors.
Nina Winter +4 more
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DNA Motif Recognition Modeling from Protein Sequences
iScience, 2018 Summary: Although the existing works on DNA motif discovery on DNA sequences are plethoric, mechanistic knowledge to infer DNA motifs from protein sequences across multiple DNA-binding domain families without conducting any wet-lab experiments is still ...
Ka-Chun Wong
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Outline of a genome navigation system based on the properties of GA-sequences and their flanks. [PDF]
PLoS ONE, 2009 Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments.
Guenter Albrecht-Buehler
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The Secret Life of the Inhibitor of Virus Replication
Viruses, 2022 The inhibitor of virus replication (IVR) is an inducible protein that is not virus-target-specific and can be induced by several viruses. The GenBank was interrogated for sequences closely related to the tobacco IVR.
Peter Palukaitis +3 more
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