The Codon Statistics Database: a Database of Codon Usage Bias
Updated: Sep 29
Krishnamurthy Subramanian1,2,‡, Bryan Payne1,‡, Felix Feyertag1 and David Alvarez-Ponce1 1 Biology Department, University of Nevada, Reno, Reno, NV, 89557. 2 Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854
We present the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq (over 15,000). The user can search for any species and access two sets of tables. One set lists, for each codon, the frequency, the Relative Synonymous Codon Usage (RSCU), and whether the codon is preferred. Another set of tables lists, for each gene, its GC content, Effective Number of Codons (ENC), Codon Adaptation Index (CAI), and frequency of optimal codons (Fop). Equivalent tables can be accessed for 1) all nuclear genes, 2) nuclear genes encoding ribosomal proteins, 3) mitochondrial genes and 4) chloroplast genes (if available in the relevant assembly). The user can also search for any taxonomic group (e.g., "primates") and obtain a table comparing all the 10 species in the group. The database is free to access without registration at http://codonstatsdb.unr.edu.