This Javascript will take a DNA coding sequence and display a graphic report showing the frequency with which each codon is used in E. coli. The data for this program are from the Class II gene data from Henaut and Danchin: Analysis and Predictions from Escherichia coli sequences in: Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C.
For a more comprehensive program, try the Graphical Codon Usage Analyzer by Thomas Schödl.

Instructions: Paste or type the coding sequence into the large textarea below (uppercase or lowercase is fine). Improper characters will be ignored; U can be put in place of T. The 'threshold' is the cutoff to display a different color for a particular codon, and for the tally of 'bad' codons.

Sequence name: Threshold: 1%5%10%15%20%25%

Enter the coding sequence:

for display:   Start: 0250500750100012501500   Codons/row: 405060708090100

Notes:

• On older machines be careful entering sequences larger than 750 bp (Javascript may run out of memory) -- you may have to split larger ORFs.
• Computation will take ~10 seconds depending on the platform.
• The resulting file can be printed, just set printer to "color/grayscale" mode.

Copyright (c) 1996/2003 Morris Maduro
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