This directory contains the Build 32 assembly of the mouse genome
(mm4, Oct. 2003) 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.
mrna.zip - Mouse mRNA from GenBank.
refMrna.zip - RefSeq mRNA from the same species as the genome.
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 incrementally updated nightly.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - Same as upstream1000, but 5000 bases.
xenoMrna.zip - All GenBank mRNA from species other than that of the genome.
mm4.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/mm4/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 files in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
mm4.chrom.sizes 2003-10-21 09:12 788
contigAgp.zip 2003-11-04 14:10 3.1M
contigFa.zip 2003-11-04 14:11 826M
contigFaMasked.zip 2003-11-04 14:12 493M
contigOut.zip 2003-11-04 14:12 145M
contigTrf.zip 2003-11-04 14:12 17M
upstream1000.zip 2003-11-04 14:12 4.5M
upstream2000.zip 2003-11-04 14:12 8.6M
upstream5000.zip 2003-11-04 14:13 21M
chromAgp.zip 2003-11-04 14:27 2.9M
chromFa.zip 2003-11-04 14:28 825M
chromFaMasked.zip 2003-11-04 14:29 492M
chromOut.zip 2003-11-04 14:29 146M
chromTrf.zip 2003-11-04 14:29 17M
est.fa.gz 2005-04-24 11:10 698M
mrna.fa.gz 2005-04-24 11:10 83M
refMrna.fa.gz 2005-04-24 11:10 15M
xenoMrna.fa.gz 2005-04-24 11:11 333M