Network construction for your target species

BiomeNet construction steps

  1. 1.Assign your project name (you will be able to retrieve your constructed network for analysis by this project name).
  2. 2.Upload protein sequences (use FASTA file) of your target species. Alternatively, you may select a NCBI sequence file located in KOBIC data server.
  3. 3.Select source networks. Although we recommend default selections for animal/plant/fungi/bacteria target species, users can conduct selection for all 95 individual source networks.
  4. 4.Press the Submit button. Network construction will be done in a few minutes for most species.

Test Run and Expected Results

  1. You may conduct test run by a single click for the following species.
  2. You may also see the expected results for the same species and perform network analysis with example gene sets.
  • Green foxtail (Setaria viridis)
  • Expected Result Green foxtail (Setaria viridis)
Assign your project name
Upload FASTA file for your target species
Browse

We recommend using one protein sequence per gene by modifying the FASTA file to contain a single protein sequence (typically the longest isoform) for each gene.
You may have a single protein sequence for each gene to remain in your input FASTA file by user-input mapping file format (example) and a Python code.

Example FASTA files
Or you may select a NCBI FASTA file for your target species
Select Source Networks

Default sets of source network species

Target species Source network species
Animals Animals, Bacteria, Fungi
Plants Animals, Bacteria, Fungi, Plants
Bacteria Bacteria
Fungi Animals, Bacteria, Fungi
Or you may select 95 source networks individually in the following list.
Animals
9 networks
4 networks
6 networks
5 networks
7 networks
Plants
7 networks
4 networks
3 networks
3 networks
4 networks
4 networks
Bacteria
7 networks
4 networks
5 networks
5 networks
4 networks
Fungi
5 networks
9 networks