This directory contains alignments of the following assemblies: - target/reference: lance-tailed manakin (GCF_009829145.1_bChiLan1.pri, 2020-01-03, Vertebrate Genomes Project) - query: Mouse (mm39, Jun. 2020 (GRCm39/mm39), Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) Files included in this directory: - md5sum.txt: md5sum checksums for the files in this directory - GCF_009829145.1.mm39.all.chain.gz: chained lastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html . - GCF_009829145.1.mm39.net.gz: "net" file that describes rearrangements between the species and the best Mouse match to any part of the lance-tailed manakin genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html . - axtNet/*.GCF_009829145.1.mm39.net.axt.gz: chained and netted alignments, i.e. the best chains in the lance-tailed manakin genome, with gaps in the best chains filled in by next-best chains where possible. The axt format is described in http://genome.ucsc.edu/goldenPath/help/axt.html . - mafSynNet/*.maf.gz - filtered net files for syntenic alignments only, in MAF format, see also, description of MAF format: http://genome.ucsc.edu/FAQ/FAQformat.html#format5 - reciprocalBest/ directory, contains reciprocal-best netted chains for GCF_009829145.1-mm39 The chainSwap program was used to translate mm39-referenced chained lastz alignments to GCF_009829145.1 into GCF_009829145.1-referenced chains aligned to mm39. See the download directory goldenPath/mm39/vsGCF_009829145.1/README.txt for more information about the mm39-referenced lastz and chaining process. Chained alignments were processed into nets by the chainNet, netSyntenic, and netClass programs. Best-chain alignments in axt format were extracted by the netToAxt program. All programs run after lastz were written by Jim Kent at UCSC. ---------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.soe.ucsc.edu, then go to the directory goldenPath/GCF_009829145.1/vsMm39/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all files in the current directory) All files in this directory are freely available for public use. -------------------------------------------------------------------- References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.