CodeOn

Screenshot of CodeOn showing amino acid usage for all CDSs in Escherichia coli K12 MG1655. CDSs are binned according to their overall DNA GC content.

Screenshot of CodeOn showing amino acid usage for all CDSs with "ATPA" in their name across all genomes in CoGe. ATPA is one of the highly conserved subunits of ATP synthase. CDSs are binned according to their overall DNA GC content.

Coding Sequence Evolution (CodeOn)

Overview

CodeOn allows you to search for CDS genomic features by name, annotation, and/or organism and display an amino acid usage table binned by the overall GC content of each CDS.

Usage

• Type in a name of a genomic feature
• Type in an annotation of a genomic feature
• Type in the name or description of an organism

Then press "search"

• When you search by genomic feature name and annotation, you can limit your search to a specific organism or set of organisms.
• If no genomic feature name or annotation is specified, but an organism or a group of organisms is, the search will get all CDSs from those organisms.

Results

The results table is organized such that:

• x-axis: CDSs are binned according to their GC content along
• y-axis: amino acids are listed according the GC content of their codons

Each cell contains:

• the relative percent usage of that amino acid for that bin
• is color-coded according to percent usage compared to all cells in the table:
  • purple: lowest
  • red: highest
  • Order: purple < blue < green < yellow < orange < red

Linking to CodeOn

• fid= CoGe database feature id. Can have multiple specified either by fid=1&fid=2&fid=3 OR fid=1::2::3
• oid= CoGe database organism id.
• accn= Feature name
• anno= Feature annotation