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Recent Announcements/Updates

  • [1/12/2012] As a heads-up, we are working on depositing a subset of RIPs reported by the 1000 genome project and adding a track for human-specific retrotransposon insertions, and will try to make them available at dbRIP in the near future.

  • [1/12/2012] A utility has been added to allow other sites to link directly to dbRIP based on dbRIP and genome ID using a format like "http://dbrip.org/cgi-bin/link2dbripByID.cgi?dbripid=1000002&genome=hg18", in which the "1000002" and "hg18" are to be replaced by the actual dbRIP ID and genome ID, respectively. Currently, this service is only available for hg18 and hg19, while the entries containing incomplete sequence (e.g. 1000001i) available only for hg19.

  • [4/2/2011] A dataset representing 483 Alu insertions with incomplete insertion sequences identified using ME-SCAN as described in Witherspoon et al, BMC Genomics 11:410, 2010 has been deposited. These entries are denoted by a letter "i" at the end of the dbRIP accession#, e.g.: "1000002i" for differentiating from the regular RIP entries. They may be upgraded to the regular entries later once complete sequence information becomes available. The data is available by setting the "sequence integrity level" to "incomplete" in SearchdbRIP. Please note that the data is only available in hg19.

  • [3/30/2011] dbRIP v2h released: added new L1 RIP data based on Kidd et al. Cell 143:837-1847, 2010 from Fosmid-end sequencing. Total entries retrieved and curated: 191 (135 novel, 56 overlapping with existing RIPs in dbRIP). The data can be checked using author name, e.g. "Kidd" or "Eichler" in SearchdbRIP

  • [10/5/2010] A new and stable dbRIP ID system is implemented in this test version. This system uses 7-digit numerical IDs, with the first digit used to indicate the major type of retrotransposons (1xxxxxx, 2xxxxxx, 3xxxxxx, 4xxxxxxx for Alu, L1, SVA and HERV, respectively). For example, dbRIP 1000001 is an Alu RIP, while 2000100 is a L1 SVA. The remaining 5 digits (5-9) are saved for new types of RIPs and for accommodating existing types that exceed 1 million in number.

  • [10/5/2010] dbRIP obtained its new and permernent URL: dbRIP.org

  • [9/1/2010] HERV RIP data is added. For HERV RIPs with the presence of both full length LTR and solo-LTR, we provide both versions of the sequences and genotype data whenever available.

  • [5/1/2010] The PositionMapping utility is added. This is useful for users with a need of comparing a list of newly identified candidate RIPs with data in dbRIP.

  • [2/1/2010] dbRIP data to hg19 is provided.

  • [12/15/2009] A test version of dbRIP with updated data (data from venter diploid genome) for both hg17 and hg18 is now available. Starting from hg18, the dbRIP ID is changed to a new system, in which a serial ID is used (e.g. "dbRIP_Alu_00001") to replace the old chr_Mbp_ID system. The new ID system provides stability not affected by the genome migration.

  • [12/01/2008] dbRIP was relocated to http://dbRIP.brocku.ca from falcon.roswellpark.org:8080/ as of January 1, 2009.
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Last modified:Friday, 11-May-2012 21:41:45 EDT .