Hi Daofeng, We suggest you ask the authors of Repeat Masker: www.repeatmasker.org.
Good luck! Katrina Learned UCSC Genome Bioinformatics Group On 9/16/11 1:04 PM, Daofeng Li wrote: > Hi Katrina, > > Thanks for your response. > actually i have read that mail before i post again to this list. > I didnot find a solution in that link.... > also in the download page > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ > is says:chromOut.tar.gz - RepeatMasker .out files (one file per > chromosome). > RepeatMasker was run with the -s (sensitive) setting. > Using: Jan 29 2009 (open-3-2-7) version of RepeatMasker and > RELEASE 20090120 of library RepeatMaskerLib.embl > i found in this linkhttp://www.girinst.org/server/archive/RepBase14.01/ > do have a > repeatmaskerlibraries-20090120.tar.gz > <http://www.girinst.org/server/archive/RepBase14.01/protected/repeatmaskerlibraries/repeatmaskerlibraries-20090120.tar.gz> > > > after download and extraction, i didnot found a L1MC name in the library > file, this really confused me > $ grep 'L1MC' Libraries/RepeatMaskerLib.embl > ID L1MC1_3end repeatmasker; DNA; ???; 1080 BP. > CC L1MC1_3end DNA > DE RepbaseID: L1MC1 > ID L1MC2_3end repeatmasker; DNA; ???; 1091 BP. > CC L1MC2_3end DNA > DE RepbaseID: L1MC2 > ID L1MC3_3end repeatmasker; DNA; ???; 2532 BP. > CC L1MC3_3end DNA > DE RepbaseID: L1MC3 > ID L1MC4_3end repeatmasker; DNA; ???; 2789 BP. > CC L1MC4_3end DNA > DE RepbaseID: L1MC4 > ID L1MC4_3endX repeatmasker; DNA; ???; 2789 BP. > CC L1MC4_3endX DNA > ID L1MC4_5end repeatmasker; DNA; ???; 2555 BP. > CC L1MC4_5end DNA > DE RepbaseID: L1MC4_5end > ID L1MC4a_3end repeatmasker; DNA; ???; 2629 BP. > CC L1MC4a_3end DNA > ID L1MC5_3end repeatmasker; DNA; ???; 1351 BP. > CC L1MC5_3end DNA > DE RepbaseID: L1MC5 > ID L1MC_orf2 repeatmasker; DNA; ???; 3294 BP. > CC L1MC_orf2 DNA > CC Description: L1MC1 consensus > ID L1MCa_5end repeatmasker; DNA; ???; 2434 BP. > CC L1MCa_5end DNA > DE RepbaseID: L1MCA_5 > ID L1MCb_5end repeatmasker; DNA; ???; 1197 BP. > CC L1MCb_5end DNA > DE RepbaseID: L1MCB_5 > ID L1MCc_5end repeatmasker; DNA; ???; 1536 BP. > CC L1MCc_5end DNA > DE RepbaseID: L1MCC_5 > CC encoding a gag protein 72% similar to L1MC4_gag > CC (80%) to L1MC4_5end from 846 to 2237 (end) > > look forward to your further response if you have. > > Thank you so much. > > On Fri, Sep 16, 2011 at 2:02 PM, Katrina Learned <[email protected] > <mailto:[email protected]>> wrote: > > Hi Daofeng, > > Please see this previously answered mailing list question: > https://lists.soe.ucsc.edu/pipermail/genome/2011-January/024826.html > > Please contact the mail list ([email protected] > <mailto:[email protected]>) again if you have any further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > On 9/16/11 9:40 AM, Daofeng Li wrote: > > Dear UCSC Genome Browser admins, > > Was the repeat consensus sequence for hg19 available for download? > as i saw in > > http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=rmsk&hgta_table=rmsk&hgta_doSchema=describe+table+schema > > <http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=rmsk&hgta_table=rmsk&hgta_doSchema=describe+table+schema> > there was a repName called L1MC, but i didnot find its sequence it > downloaded Repbase fasta files > > i also noticed that "UCSC has used the most current versions > of the > RepeatMasker software and repeat libraries available to > generate these data. > Note that these versions may be newer than those that are > publicly available > on the Internet. > " > So might be these difference caused my problem. Is there any > place for > download or could you provide me with this file？ > > Thanks for your help > > Best wishes. > > > > > -- > Daofeng > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
