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SAGE Genie
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Cancer Genome Characterization Initiative

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DK Microbe

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What the DK Microbe Tool Can Do

Given a set of 17 base-pair digital karyotyping tags, the DK Microbe tool searches for exact matches to virtual tags in the genomes of 2565 bacterial and viral genomes.

You may query for matches to a small number of tags by entering the tags directly in a text box (multiple tags are separated by commas). Alternatively, longer lists of tags to be matched may be uploaded in a file. Note that microbial tags that are exact matches to human digital karyotyping tags have been removed from the set of virtual microbial tags.

For a description of the bacterial and viral digital karyotyping virtual tag sets, see the following:

Chris G. Duncan, Rebecca J. Leary, Jordan Cummins, Jimmy Cheng-Ho Lin, Chunhui Di, Carl F. Schaefer, Tian-Li Wang, Darell Bigner, Levy Kopelovich, Bert Vogelstein, Ken Kinzler, Victor E. Velculescu, and Hai Yan. Identification of microbial DNA in human cancer. (Submitted)
For a detailed description of the digital karyotpying method, see the following:
Tian-Li Wang, Christine Maierhofer, Michael R. Speicher, Christoph Lengauer, Bert Vogelstein, Kenneth W. Kinzler, and Victor E. Velculescu. Digital karyotyping. PNAS 99(25):16156-16161.
Additional information about digital karyotyping can be found at www.digitalkaryotyping.org

Use the DK Microbe


By entering tags
   
2. Submit query:
By uploading a file of tags
   
2. Submit query:

Upload File Format

  • The text file must list the human tags in a vertical column like this:
    AAGCCTTTAGGAATGAA
    TTCGATCGTGCGATGTC
    GAGCGGGCCTACCCGAC
    GGCACGCCGGCCCGGAG
    CGTACGCCGAAAAGCAG
    GCCTCCCTGGGATCCGA
    


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