RCDI/eRCDI statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RCDI/eRCDI
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Tool usage distribution map

This map represents all the scientific publications referring to RCDI/eRCDI per scientific context
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Associated diseases

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Protocols

RCDI/eRCDI specifications

Information


Unique identifier OMICS_22349
Name RCDI/eRCDI
Alternative name Relative Codon Deoptimization Index / Expected RDCI
Interface Web user interface
Restrictions to use None
Input data Some sequences, a codon usage table and the genetic code.
Input format FASTA
Output data Genes’ parameters: the RCDI values, the frequencies for all codons [(CiFa/CiFh) Ni;] and the %G+C of each gene; Global parameters: the mean %G+C and amino acid composition, and the number of sequences used to calculate the eRCDI; Statistical tests; and Expected RCDI: the mean RCDI value from random sequences and the eRCDI value.
Programming languages PHP
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pere Puigbò

Information


Unique identifier OMICS_22349
Name RCDI/eRCDI
Alternative name Relative Codon Deoptimization Index / Expected RDCI
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 1.4
Stability Stable
Requirements
tcl/tk
Maintained Yes

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Maintainer


  • person_outline Pere Puigbò

Publication for Relative Codon Deoptimization Index / Expected RDCI

RCDI/eRCDI citations

 (3)
library_books

Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

2018
PMCID: 5915587
PMID: 29691381
DOI: 10.1038/s41426-018-0079-0

[…] The RCDI value of eight segmented complete coding sequences of H3N2 CIV strains were calculated by the RCDI/eRCDI SERVER (http://genomes.urv.cat/CAIcal/RCDI/). The five non-bias codons were excluded. The reference codon usage table of potential hosts was obtained from the codon usage database (http://w […]

call_split

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution

2017
BMC Genomics
PMCID: 5568313
PMID: 28830350
DOI: 10.1186/s12864-017-4063-1
call_split See protocol

[…] imization index (RCDI) compares the similarity in codon usage of a given coding sequence with that of a reference genome. The RCDI values for the polymerase genes of EIV were computed using web-based RCDI/eRCDI server (http://genomes.urv.es/CAIcal/RCDI/). This server also calculates expected RCDI values for a set of sequences by generating random sequences with similar G + C content and amino acid […]

call_split

Evolution of codon usage in Zika virus genomes is host and vector specific

2016
PMCID: 5117728
PMID: 27729643
DOI: 10.1038/emi.2016.106
call_split See protocol

[…] the ZIKV coding sequences were calculated to determine the codon deoptimization trends by comparing the similarity in codon usage of a given coding sequence with that of a reference genome using the RCDI/eRCDI server. An RCDI value of 1 indicates that the virus follows the host codon usage pattern and displays a host-adapted codon usage pattern. Conversely, RCDI values higher than 1 indicate the […]


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RCDI/eRCDI institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Department of Microbiology, University of Barcelona, Barcelona, Spain; Department of Biochemistry and Biotechnology, Nutrigenomics Research Group, Rovira i Virgili University, Tarragona, Spain
RCDI/eRCDI funding source(s)
Supported by the Department of Health and Human Services intramural program (National Institutes of Health, National Library of Medicine).

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