• Genome wide target prediction for MBStar (Click here to Download)
  • Executable

    (NOTE: THIS SOFTWARE IS FREELY AVAILABLE FOR ACADEMIC USE ONLY)

    Download Instructions:

    • Download the MBStar package.
    • Unzip and extract all its files.
    • Go to MBStar directory. Type 'chmod +x MBStar' and 'chmod +x MIL-Forest'.
    • Type: ./MBStar -test < filename > -3utr < filename > -mir < filename > to execute MBStar.

    Usage:

    • Type: ./MBStar --help to see its usage.
    • Parameters:

      test file: A Tab delimited two columns input file. First column contains the miRNA name (ex: >hsa-miR-155-5p) and the second column contains the Refseq id (ex: NM_182715) of mRNA. The last line of file should end with a '>'.
      3utr file: A fasta format file containing the 3'UTR sequences.
      mir file: A fasta format file containing the miRNA sequences.

      Download zip file contains:

    • hg19_3utr.txt: Human 3'UTR database file.
    • mirbase_hsa_latest.txt: MicroRNA sequence file.
    • positive_train_instance_index: An index file to train the classifier.
    • negative_train_instance_index: An index file to train the classifier.
    • positive_train40: Data file for training the classifier.
    • negative_train40: Data file for training the classifier.
    • config.conf: Configuration file for classifier.
    • MBStar_example.txt: Some example interactions for MBStar.

    • The result is obtained by the following command:
      ./MBStar -test MBStar_example.txt -3utr hg19_3utr.txt -mir mirbase_hsa_latest.txt
      The result is saved in the file named: MBStar_predicted_binding_sites.txt

      Result:

      The result colomns are as follows:

    • col1: miRNA Name
    • col2: mRNA Name
    • col3: Binding sites with flanking regions
    • col4: miRNA Sequence
    • col5: Site type
    • col6: Binding position
    If you have any questions or difficulties running this webserver please contact: dipg at isical dot ac dot in