Predict_RBP specifications

Information


Unique identifier OMICS_18539
Name Predict_RBP
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://cic.scu.edu.cn/bioinformatics/Predict_RBP.rar
Maintained Yes

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Maintainer


  • person_outline Menglong Li <>

Publication for Predict_RBP

Predict_RBP in publications

 (9)
PMCID: 5899451
PMID: 29581298
DOI: 10.1073/pnas.1719138115

[…] we also collected rnase footprints from hela cells, which demarcate protein-bound regions of the transcriptome at single-nucleotide resolution transcriptome-wide and can, therefore, be used to predict rbp binding sites (). we focused on footprints that are likely to be involved in gene regulation by filtering the footprints to only include those that were in the 5′ or 3′ utrs […]

PMCID: 5331642
PMID: 28245811
DOI: 10.1186/s12859-017-1561-8

[…] features from large-scale data [], which is also a recent popular choice for constructing the computational models. for example, the deepnet-rbp fuses the structural and k-mer sequence features to predict rbp interaction sites [] using dbns. dann trains a dbn to annotate non-coding variants [], which is able to capture non-linear abstraction features. we also developed a model called ipminer […]

PMCID: 5282898
PMID: 28143578
DOI: 10.1186/s12943-017-0598-7

[…] tissues and possible mirna regulated networks [, ]. the circinteractome database contains corresponding genome sequences, primers for qrt-pcr, and sirnas of mature circrnas. it can also be used to predict rbp binding sites []. the circpedia and tscd databases contain rna-seq data of several human cell lines and samples [, ].table 1 , unlike linear rna, 3′ and 5′ terminals are not exposed […]

PMCID: 4894278
PMID: 26787667
DOI: 10.1093/bioinformatics/btw003

[…] largest integrative analysis in the number of rbps and different data sources used. the analysis included a compendium of 31 published clip experiments on 19 rbps and other genomic data sources to predict rbp crosslinking sites at a nucleotide-resolution. we discovered discriminative patterns across different data sources and learned a comprehensive model of protein–rna interaction […]

PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639

[…] kyg[], prbr[], pprint[], dnabindprot[], protedna[], displar[], dr_bind1[], aarna[], rbscore[], rbrdetector[], dnabind[], xypan[] and rnaprosite (lilab.ecust.edu.cn/nabind/), while the programs are predict_rbp[], prna[] and rbrident[]. previously reported prediction approaches have been summarized in . slow programs dr_bind1 and rbrdetector were only tested on part of the datasets […]


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Predict_RBP institution(s)
Key Laboratory of Green Chemistry and Technology, College of Chemistry, Ministry of Education, Sichuan University, Chengdu, China
Predict_RBP funding source(s)
Supported by the National Natural Science Foundation of China (No. 20775052).

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