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.
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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 <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
mm5.chrom.sizes 2004-06-27 20:25 777
chromAgp.zip 2004-07-14 14:53 3.2M
chromOut.zip 2004-07-14 14:56 146M
chromFa.zip 2004-07-14 15:27 823M
chromFaMasked.zip 2004-07-14 15:43 488M
contigAgp.zip 2004-07-14 15:44 3.4M
contigOut.zip 2004-07-14 15:46 145M
contigFa.zip 2004-07-14 16:16 824M
contigFaMasked.zip 2004-07-14 16:35 488M
chromTrf.zip 2004-07-14 16:35 16M
contigTrf.zip 2004-07-14 16:36 17M
upstream1000.zip 2004-07-14 21:04 4.7M
upstream2000.zip 2004-07-14 21:06 9.0M
upstream5000.zip 2004-07-14 21:09 22M
mrna.fa.gz 2008-07-25 01:48 127M
xenoMrna.fa.gz 2008-07-25 01:52 564M
est.fa.gz 2008-07-25 02:12 784M
refMrna.fa.gz 2008-07-25 02:12 21M