Hello Andrew, The conservation track would be a better choice. Examine the methods/contents in the browser and then use the Downloads server to obtain the data.
For hg19, the data can be found here: 1) http://hgdownload.cse.ucsc.edu/downloads.html 2) Human -> Multiple Alignments (four sub-tracks) A utility in the kent source tree can help to subset by species: mafFilter with the option -speciesFilter used. Utility descriptions: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities Pre-compiled: http://hgdownload.cse.ucsc.edu/admin/exe/ Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/5/10 10:19 AM, Yi, Andrew wrote: > Dear Sir/Madam > > I am looking source files for tables in synteny that contain all conserved > synteny regions (chr and nucleotide sequence locations) between the genomes > of two organisms (human and mouse). > > It seems that both axtNet/*.hg19.mm9.net.axt.gz > and syntenicNet/*.hg19.mm9.synNet.axt.gz > have required info, > e.g. > chr1.hg19.mm9.synNet.axt.txt > 0 chr1 405402 405580 chr1 18566119 18566283 - 3972 > YYI: seems right, but the format very similar to chr1.hg19.mm9.net.axt.txt > 175 chr1 405402 405580 chr1 18566119 18566283 - 3972 > but not all records are identical. > > can you explain why? > and which file is best for my purpose? > > > Andrew > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
