NCI RID Tools

  1. ISmapper
    • ISmapper is a program designed to map retrovirus integration sites to their host genes. The program displays provirus LTRs in the context of the host genome to facilitate PCR primer design and to aid cloning of the inserted provirus. This is a standalone tool. The submitted file will not be stored in the database.
    • To use this tool, users need to
      • Select the virus from the virus pull down menu
      • Upload a text file containing the original ID, chromosome number, integration site, and provirus orientation in each line. For example:
      • original_idchrinsert_positioninsert_orientation
        1chr1 15009253+
        2chr9 13555399+
        3chr6 3430489-
        Note: Each item should be separated by a tab.
      • Click submit.
      • To display the integration site and the flanking host sequences, click "I" button in the result page.
      • Please limit the number of input sites to < 200, 000.
  2. VIGE -- Virus integration and host gene expression analysis
    • VIGE is a tool used to display the distributions of virus integration sites and host gene expression level.
    • To use this tool, users need to enter their own gene expression data and provirus integration data, or select a sample from the list.
    • To use your own data, two files need to be uploaded. Each file, the gene expression data file and the integration data file need to be in tab delimited text files.
        The format of the gene expression file:
        Gene nameChromosomeMIDTSSTENDExpression
        MIR1302-1013033229554311090
        FAM138A135318345543608126
        OR4F5169550690917000866
        RP11-34P13.8190328895519110524
        Note: MID: middle point of gene transcript location; TSS: Transcript start site; TEND: Transcription stop site.
        The format of Virus integration site file:
        ChromosomeIntegration site
        1568829
        1718597
    • This tool has 3 options
      • Full chromosome: this option will display integration sites and gene expression in a full length chromosome. To use this option, users need to select a chromosome.
      • Partial chromosome: this option will display integration sites and gene expression within a range of a chromosome. To use this option, users need to select a chromosome, enter a start position and an interval in million bases.
      • A specific gene: this option will display integration sites and gene expression for a specific gene. If users leave the flanking region blank, the exact length of the selected gene will be displayed. If users enter a flanking region in million base, the selected gene and its flanking region will be displayed. To use this option, leave chromosome, start position, and interval blank.



If there are any questions, please contact Wei Shao at rid@mail.nih.gov

© RID. Supported by Advanced Biomedical Computing Center at Leidos/FNLCR.