Hello Andrew, Since you are looking for synteny information, syntenicNet/*.hg19.mm9.synNet.axt.gz is most likely what you need, as they contain the human/mouse alignments after syntenic filtering. If, however, you are interested in doing your own syntenic filtering, the axtNet data would more likely suit your needs.
You can read more about the axt format here: http://genome.ucsc.edu/goldenPath/help/axt.html You should be able to download these files directly form the downloads page, or through ftp. I hope this clears things up. Please feel free to contact us again. Antonio Coelho UCSC Genome Bioinformatics Group -------- Original Message -------- Subject: RE: [Genome] source files for synteny regions Q2 Date: Thu, 6 May 2010 10:18:06 -0500 From: Yi, Andrew <[email protected]> To: Jennifer Jackson <[email protected]> Thanks Jennifer, I visited hgdownload -> human But I don't need multiple alignments, Multiple Alignments for 45 genomes: Multiple alignments of 45 vertebrate genomes with Human Conservation scores for alignments of 45 vertebrate genomes with Human Basewise conservation scores (phyloP) of 45 vertebrate genomes with Human FASTA alignments of 45 vertebrate genomes with Human for CDS regions What I need is human (hg19) and mouse (mm9) synteny region translation, which seems to be http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsMm9/ two database files are likely my targets, axtNet/*.hg19.mm9.net.axt.gz syntenicNet/*.hg19.mm9.synNet.axt.gz but I don't know which one is better? I also visit Utility Utility descriptions: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities I did not find any useful information to show me downloading instruction. Andrew -----Original Message----- From: Jennifer Jackson [mailto:[email protected]] Sent: Wednesday, May 05, 2010 1:43 PM To: Yi, Andrew Cc: [email protected] Subject: Re: [Genome] source files for synteny regions 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
