RCDI/eRCDI statistics

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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 in publications

 (3)
PMCID: 5915587
PMID: 29691381
DOI: 10.1038/s41426-018-0079-0

[…] that the codon usage bias of the strain is significant and more adaptable to that host., 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 […]

PMCID: 5568313
PMID: 28830350
DOI: 10.1186/s12864-017-4063-1

[…] 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 […]

PMCID: 5117728
PMID: 27729643
DOI: 10.1038/emi.2016.106

[…] 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 […]


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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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