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CAIcal specifications

Information


Unique identifier OMICS_22384
Name CAIcal
Alternative name Codon Adaptation Index cal
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A DNA sequence, protein alignment, codon usage table.
Input format FASTA
Output data Nucleotide composition, codon usage, codon usage per thousand and/or Relative Synonymous Codon Usage (RSCU), Codon Adaptation Index (CAI).
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Pere Puigbò
  • person_outline Ignacio Bravo
  • person_outline Santiago Garcia-Vallve

Information


Unique identifier OMICS_22384
Name CAIcal
Alternative name Codon Adaptation Index cal
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainers


  • person_outline Pere Puigbò
  • person_outline Ignacio Bravo
  • person_outline Santiago Garcia-Vallve

Publication for Codon Adaptation Index cal

CAIcal citations

 (63)
library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] based on housekeeping genes were very similar to those found with the table from codon usage database with generic human genes. the cai values for each sequence from zikv genes were calculated with caical program (http://genomes.urv.es/caical/). we assessed the confidence of cai estimates by the calculation of expected cai values for 1000 random sequences with similar gc-content […]

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 cai value by reference codon usage database of the different potential hosts ranged from 0 to 1. the calculation method was performed as previously described (http://genomes.urv.cat/caical/rcdi/), and the five non-bias codons were excluded. high values indicate that the codon usage bias of the strain is significant and more adaptable to that host., the rcdi value of eight […]

library_books

Full Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus

2018
Viruses
PMCID: 5923487
PMID: 29652824
DOI: 10.3390/v10040193

[…] for each isolate. to calculate normalized cai, full-length polyprotein sequences of west african bagv isolates and previously available bagv sequences from spain were compared to that of human using caical v1.4 program (http://genomes.urv.es/caical/) []. first, we obtained a “raw” cai (rcai) and then, the cai was normalized by the “expected neutral cai” (ecai) value based on 1000 random viral […]

library_books

Does adaptation to vertebrate codon usage relate to flavivirus emergence potential?

2018
PLoS One
PMCID: 5792106
PMID: 29385205
DOI: 10.1371/journal.pone.0191652

[…] polyprotein was used to calculate cai. for tobacco mosaic virus, coding regions were concatenated into frame and then used to generate cai values., to calculate normalized cai, we first used the caical program [] to obtain a “raw” cai (rcai). next, an “expected neutral cai” (ecai) value was calculated by generating 1000 random sequences using similar length, codon composition and gc-content. […]

library_books

Disentangling the Causes for Faster X Evolution in Aphids

2018
Genome Biol Evol
PMCID: 5798017
PMID: 29360959
DOI: 10.1093/gbe/evy015

[…] u tests. finally, we tested the factors affecting log-transformed dn/ds using a complete linear model. included variables in model 1 were cds size, cai (the codon adaptation index, calculated with caical, ), τ (a measure of morph specificity in expression, ), mean expression level (averaged over the three morphs), and chromosome. to test whether dn/ds measures were significantly higher […]

library_books

Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus

2017
Oncotarget
PMCID: 5746386
PMID: 29299151
DOI: 10.18632/oncotarget.22738

[…] of the different host animals were obtained using an online tool (http://www.kazusa.or.jp/codon/). to estimate the codon adaption of the mers to the host, the cai value is calculated using the caical software (http://genomes.urv.es/caical). in the analysis, the synonymous codon usage pattern of the viral host were deposited as the reference and the cai values of the mers and mers related […]


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CAIcal institution(s)
Department of Biochemistry and Biotechnology, Rovira i Virgili University (URV), Tarragona, Spain; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Experimental Molecular Evolution, Institute for Evolution and Biodiversity, University of Muenster, Germany
CAIcal funding source(s)
Supported in part by the Intramural Research Program of the National Institutes of Health, National Library of Medicine, the Volkswagen Stiftung in the program Evolutionary Biology.

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