Ipro54-pseknc: A sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition
Open accessAbstract
The σ(54) promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ(54) promoters. Here, a predictor called 'iPro54-PseKNC' was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called 'pseudo k-tuple nucleotide composition', which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ(54) promoters.
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- Authors
- Lin, H., Deng, E.-Z., Ding, H., Chen, W., & Chou, K.-C.
- Affiliations
- University of Electronic Science and Technology of China (CN)
- North China University of Science and Technology (CN)
- King Abdulaziz University (SA)
- Corresponding author
- Lin, Hao
- Chen, Wei
- Chou, Kuo-Chen
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-10-31
- Volume
- 42
- Issue
- 21
- Pages
- 12961-12972
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4245931
- OpenAlex
- W2124266758
- Cited by
- 508
- References
- 97
- Citations by year
- 2026: 8 · 2025: 14 · 2024: 16 · 2023: 15 · 2022: 26 · 2021: 31 · 2020: 41 · 2019: 64 · 2018: 90 · 2017: 54 · 2016: 78 · 2015: 66 · 2014: 5
- FWCI
- 27.76
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Fundamental Research Funds for the Central Universities (61202256, 61100092, ZYGX2013J102, ZYGX2012J113, 61301260, C2013209105)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- promoter identification, prokaryotic transcription, incremental feature selection, transcription start sites, translation initiation sites, gamma distribution, web server
- MeSH terms
- Nucleotides, Peptide Chain Initiation, Translational, Promoter Regions, Genetic, Software, Genome, Bacterial, Sequence Analysis, DNA, Transcription Initiation Site, RNA Polymerase Sigma 54
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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