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Cited by 0RNA Research and SplicingGenomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

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PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates

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Wei, Xinhang, Duan, Yingtian, Li, Danyang, Liu, Xudong, Xie, Juan, Liu, Shiyong·2026·BMC Genomics
DOI 10.1186/s12864-026-12657-3PMC PMC13032426

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Abstract

In this paper, we present PRIME-BSPre, a template-based genome-wide method for predicting protein-RNA binding sites that incorporates the RNA sequence and secondary structure as well as the tertiary structure of corresponding RBPs. We are pioneers in introducing low Shannon entropy algorithm in PRIME-BSPre to describe the binding preferences of RBPs on RNA motifs. The LS-PEAK derived from LS-Scores in PRIME-BSPre is utilized to optimize the alignments screening. PRIME-BSPre has been successfully benchmarked on the human genome, demonstrating its excellent prediction performance on independent RBP datasets and its robustness across different cell lines.

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Metadata

Authors
Wei, X., Duan, Y., Li, D., Liu, X., Xie, J., & Liu, S.
Affiliations
Huazhong University of Science and Technology (CN)
Corresponding author
Liu, Shiyong
ORCID
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2026-02-21
Volume
27
Issue
1
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/s12864-026-12657-3
PMC
PMC13032426
OpenAlex
W7130849569
Cited by
0
References
3
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Natural Science Foundation of China (32271267)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
RNA-binding proteins, template-based modeling, RNA secondary structure, RNA tertiary structure, RNA motifs, genomic prediction, human genome
MeSH terms
Prediction Algorithms, Algorithms, Binding Sites, Humans, Nucleic Acid Conformation, Protein Binding, RNA, Genome, Human, RNA-Binding Proteins, Computational Biology, Genomics

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