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Le Huang edited this page Feb 19, 2023 · 2 revisions
  • V3.0.7
  1. 3.0.7 Fix the bug in cgc_parser.py.
  2. hmmdb, cazydb, tf-1, tf-2, stp and tcdb are updated.

  • V3.0.6 We now create the bioconda version. To old users, please run conda install dbcan -c bioconda for update from now on. To new users, please follow the installation instruction below. 1.

    conda create -n run_dbcan python=3.8 dbcan -c conda-forge -c bioconda
conda activate run_dbcan
    1. Rename the code hmmscan-parser.py to hmmscan_parser.py

  • V3.0.5 please use pip install dbcan==3.0.5 for update

    1. Fixed the bug in signalP
    2. Fixed the cgc problems and run_dbcan small bugs.

  • V3.0.4 please use pip install dbcan==3.0.4 for update

    1. Fixed eCAMI tool problem.
    2. If you download gff file from NCBI, please check the last column, replace Name with ID, and ID with Name.

  • V3.0.2 please use pip install dbcan==3.0.2 for update

    1. Added eCAMI tool, remove Hotpep from run_dbCAN;
    2. Changed the format of cgc.out to make it easy to read;
    3. Fixed ‘-t all’ will cause the program to generate empty files.
    4. Updated CAZy db for Diamond and HMMER DB for HMMER.
    5. Re-arranged the code. The command line is run_dbcan without the suffix .py. Please check the command lines below.
    6. The database files under db folder is now hosted through Git-LFS. To download the complete db files, please use the command git lfs pull (Note: To use git lfs, please check the installation guide at https://git-lfs.github.com/).
    7. Docker file is updated and we simplify the installation step.

  • v2.0.11 please use pip install run-dbcan==2.0.11 for update

    1. Add ec number prediction to hotpep result;
    2. 04/21/2020 dbCAN2 Hotpep PPR patterns updated to most recent release of CAZyDB (2019). Also missing group EC# files for families added in;
    3. Revising the output name file in hotpep as random number, to make the program more robust for paralleing running.
    4. Prioritizing the CAZyme prediction over TF/TC/STP prediction when preparing gff input file for CGC-Finder.
    5. Rewrite the installation steps. Recommend user to use customized virtual environment (use certain python version).
    6. Fix the duplicate ACC of tf-2.hmm to make it compatiable for the newest hmmer (3.3). Delete version limitatino to hmmer.
    7. Fix the prodigal predicted gff file end with ";" problem.

  • v2.0.6 released on Feb 17, 2020, please use pip install run-dbcan==2.0.6 for update We forgo FragGeneScan because this program does not work now. We use Prodigal instead. So, you don't need to use conda install fraggenescan now. We add extra information EC number to the last columns of Hotpep output to make it consistent with previous Hotpep result.

  • 10/08/2019 We create a python package. Be sure to install Anaconda or Miniconda first, and then use the following commands to install our program one time. We strongly recommend you to use virtual environment to seperate your own system and this executive scripts. Please make sure to use conda install -c bioconda diamond hmmer prodigal and database installation script to have the appropriate dependencies and database installed and configured. Thanks for suggestion and contribution from tesujimath .

  • 04/15/2019 We created a docker image of run_dbcan. Make sure to install docker properly. Thanks for suggestion and contributions from Haidyi.

  • 1/10/2019 We rewritted program and added stp hmmdb signature gene in CGC_Finder.py (stp means signal transduction proteins; the hmmdb was constructed by Catherine Ausland of the Yin lab at NIU). Then Change tfdb from tfdb to tf.hmm, which is added to db/ directory (tfdb was a fasta format sequence file, which contains just bacterial transcription factor proteins; tf.hmm is a hmmer format file containing hmms downloaded from the Pfam and SUPERFAMILY database according to the DBD database: http://www.transcriptionfactor.org). Also, our project updates dbCAN-HMM db(V8) and CAZy db. Furthermore, we fixed bugs in HotPep python version to fit python 3 user. Last but not least, we added certain codes to make it robust. Thanks for hmmscan-parser.py suggestion from Mick.

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