This directory contains the Build 33 assembly of the mouse genome (mm5, May 2004) from the Mouse Genome Sequencing Consortium. This assembly was produced at NCBI. Files included in this directory: chromAgp.zip - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.zip - The assembly sequence in one file per chromosome. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. RepeatMasker June 2003 version with RepBase libraries: RepBase Update 8.4, RM database version 20030619 chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period of less than or equal to 12, and translated into one .bed file per chromosome. contigAgp.zip - Description of how the assembly was generated from fragments at a contig layout level. contigFa.zip - The assembly sequence contig, in one file per contig. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. contigFaMasked.zip - The assembly sequence contigs, in one file per contig. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. contigOut.zip - RepeatMasker .out file for contigs. These were created by RepeatMasker at the -s sensitive setting. contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per contig. est.fa.gz - Mouse ESTs from GenBank, updated once a week via automatic GenBank updates. mrna.fa.gz - Mouse mRNA from GenBank, updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome, updated once a week via automatic GenBank updates. upstream1000.zip - Sequences 1000 bases upstream of annotated transcription start of RefSeq genes. This includes only the cases where the transcription start is annotated separately from the coding region start. Note that upstream files are generated only when an assembly is released. Therefore, the data may be slightly out of synch with the RefSeq data in assemblies that are updated nightly. upstream2000.zip - Same as upstream1000, but 2000 bases. upstream5000.zip - Same as upstream1000, but 5000 bases. xenoMrna.fa.gz - GenBank mRNA from species other than that of the genome, updated once a week via automatic GenBank updates. mm5.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ----------------------------------------------------------------- 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.cse.ucsc.edu, then go to the directory goldenPath/mm5/bigZips/. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the tables in this directory are freely usable for any purpose.