What is dbCAN2 meta server?

dbCAN2 meta server is a web server for automated Carbohydrate-active enzyme ANnotation, funded by the National Science Foundation (DBI-1652164). Similar resources on the web include CAZy, CAT (obsolete), and Hotpep. dbCAN2 meta server is an updated version of the original dbCAN web server (obsolete), and has the following new features (thanks to dbCAN users all over the world for suggestions):

  • dbCAN2 meta server allows submission of nucleotide sequences: prokaryotic genomic sequences (fna file) of draft genomes and metagenomes; for eukaryotic genomes, please still submit protein seqs (faa file)
  • dbCAN2 meta server integrates three state-of-the-art tools/databases for automated CAZyme annotation:
    1. HMMER for annotated CAZyme domain boundaries according to the dbCAN CAZyme domain HMM database
    2. DIAMOND for fast blast hits in the CAZy database
    3. Hotpep for short conserved motifs in the PPR library
  • dbCAN2 meta server can identify transcription factors (TFs), transporters (TCs), and further CAZyme gene clusters (CGCs) using CGC-Finder if users submit faa+gff files or fna file
  • dbCAN2 meta server combines the results from the three tools and allows visualization as venn diagram and detailed results as graphs

dbCAN2 meta server will be updated once a year to use the most updated CAZy database, dbCAN HMM database and Hotpep peptide database

News

  • 8/17/2021: dbCAN HMMdb v10 is released (based on CAZyDB 7/26/2020). Now the HMMdb contains 692 CAZyme HMMs (445 family HMMs + 3 cellulosome HMMs + 244 subfamily HMMs). The CAZyDB for Diamond search is also updated, containing in total 1,776,583 fasta sequences. See readme for details.
  • 04/28/2021: We received an NIH R01 award to continue the development of dbCAN family tools
  • 8/04/2020: dbCAN HMMdb v9 is released (based on CAZyDB 7/30/2020). Now the HMMdb contains 681 CAZyme HMMs (434 family HMMs + 3 cellulosome HMMs + 244 subfamily HMMs). The CAZyDB for Diamond search is also updated, containing in total 1,716,043 fasta sequences. See readme for details.
  • 04/21/2020: dbCAN2 Hotpep PPR patterns updated to most recent release of CAZyDB (2019). Also missing group EC# files for families added in.
  • 10/07/2019  run_dbcan python package   is released. You should not only use pip install run-dbcan==2.0.0 to download it, but also install Miniconda or Anaconda as well to install dependencies packages(conda install -c bioconda diamond hmmer=3.1b2 prodigal fraggenescan). And then use only one command to download and compress all the related databases from Download section. Read more on run_dbcan2.
  • /08/2019: dbCAN HMMdb v8 is released (based on CAZyDB 7/26/2019). Now the HMMdb contains 641 CAZyme HMMs (421 family HMMs + 3 cellulosome HMMs + 217 subfamily HMMs). The CAZyDB for Diamond search is also updated, containing in total 1,386,849 fasta sequences. See readme for details.
  • 4/01/2019: dbCAN2 has a docker version written by Haidong Yi.
  • 3/19/2019: dbCAN2 web server has moved to UNL and has a new URL
  • 1/20/2019: dbCAN2 standalone package is available on github; if you prefer to still use the old hmmscan way, the data are available in the download page
  • 8/25/2018: dbCAN HMMdb v7 is released (based on CAZyDB 7/31/2018): HMMs of 15 new families were added (AA14, AA15, CBM82, CBM83, GH146, GH147, GH148, GH149, GH150, GH151, GH152, GH153, GT105, GT106, PL28), GT2 family HMM now is replaced with 8 Pfam HMMs (GT2_Chitin_synth_1, GT2_Chitin_synth_2, GT2_Glycos_transf_2, GT2_Glyco_tranf_2_2, GT2_Glyco_tranf_2_3, GT2_Glyco_tranf_2_4, GT2_Glyco_tranf_2_5, GT2_Glyco_trans_2_3)
  • 5/2/2018: dbCAN2 meta server paper is accepted to publish at Nucleic Acids Research
  • 8/15/2017: Tanner and Le Huang begin to work on dbCAN2 meta server
  • 7/1/2017: Yanbin is awarded the NSF CAREER grant for CAZyme bioinformatics research