Co-occurrence of Enzyme Domains (CO-ED) analysis web server

Based on an article in Nature Chemical Biology by Tristan de Rond, Julia Asay, and Bradley Moore.

This tool is a work-in-progress. Please raise issues or ask questions in the discussion group.

Code for the Jupyter Notebook version is available at github.com/tderond/CO-ED.

This tool generates files that need to be opened in Cytoscape, which is free open source software. (Instructions)

Job Submission

Job title

E-mail address (optional)
Your e-mail address will be used only to send you status updates on this job, nothing else. For general updates on the web tool, please join the discussion group

Select a job type:

CO-ED from pre-annotated domains (0 jobs currently in queue)
Annotate domains in protein FASTA using HMMER, then run CO-ED (0 jobs currently in queue)

For typical bacterial proteomes, running just CO-ED should take a minute or so (not counting time spent in the queue), but annotating domains will take longer, depending on how many domains are selected (for the default selection, expect around 10 minutes).

Input required for this job:

Secondary input

Optional. Adds extra information to your CO-ED network

secondary input 1

Input type for secondary input 1:
none
pfamscan output (plain text format)
hmmsearch tabular output (use --tblout in hmmsearch command line)
protein FASTA
all of Uniprot (pre-computed)

secondary input 2

Input type for secondary input 2:
none
pfamscan output (plain text format)
hmmsearch tabular output (use --tblout in hmmsearch command line)
protein FASTA
all of Uniprot (pre-computed)

secondary input 3

Input type for secondary input 3:
none
pfamscan output (plain text format)
hmmsearch tabular output (use --tblout in hmmsearch command line)
protein FASTA
all of Uniprot (pre-computed)

Select which domains to consider for analysis:

The table is pre-loaded with information from Pfam-A, and a curated set of enzyme domains is pre-selected. You can modify the selection as well as the Names, Descriptions, Clan memberships, etc., to your liking by interacting with the table below.

If your pfamscan or hmmsearch input files contain domains not in Pfam-A, you can add those domains to the table and select them to consider them in the analysis. It is currently not possible to do domain annotations from protein FASTA on domains not in Pfam-A. If this is a feature you would like to see, please let us know.

The domains will be matched by their accession numbers, not considering any version numbers after the dot.

If multiple domains part of the same Clan match in the same protein, only the one with the lowest E value will be considered.

Separate multiple categories by commas and/or whitespace. Only affects the domains that pass the filter below

please wait while domain table is loading...

(new row is appended at the end of the table)