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Protocols

RNABindRPlus specifications

Information


Unique identifier OMICS_03026
Name RNABindRPlus
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Publication for RNABindRPlus

RNABindRPlus citations

 (3)
call_split

The HEX 110 Hexamerin Is a Cytoplasmic and Nucleolar Protein in the Ovaries of Apis mellifera

2016
PLoS One
PMCID: 4783013
PMID: 26954256
DOI: 10.1371/journal.pone.0151035
call_split See protocol

[…] Potential RNA-binding sites were searched in the HEX 110 sequence using RNABindR, BindN, PPRint, SVM and RNABindRPlus softwares [–]. We selected the most significant motifs, and only the alignments passing a threshold of 80% were considered as significant. The cNLS Mapper tool (http://nls-mapper.iab.keio […]

library_books

Direct Evidence for Packaging Signal Mediated Assembly of Bacteriophage MS2

2016
J Mol Biol
PMCID: 4751978
PMID: 26608810
DOI: 10.1016/j.jmb.2015.11.014

[…] ession P03610 query and homologous UniRef sequences identified by the server. CP secondary structures were taken from the annotation of PDB file 2MS2.RNA-binding sites in MPs were predicted using the RNABindRPlus server with sequence accessions MS2 (P03610), R17 (EF108465), JP501 (AAF67668), phage fr (CAA33135), BZ13 (FJ483837), KU1 (AAF67673), GA (CAA27496), C-1-INW (AFN37812), Hgal1 (AFN37816), […]

call_split

A Large Scale Assessment of Nucleic Acids Binding Site Prediction Programs

2015
PLoS Comput Biol
PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639
call_split See protocol

[…] Li lab and Xiaoyong Pan provided RNAProSite and xypan prediction results respectively, with default parameter. aaRNA was used by inputting the structure file with default parameters. RNABindR and RNABindRPlus were predicted with default parameters, while removing 95% sequence identity in RNABindRPlus. KYG was predicted with command line using “method_type = 8” option. RBscore_SVM was based on […]

Citations

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RNABindRPlus institution(s)
Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA

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