This directory contains the v.1.0 Mmul_051212 rhesus genome assembly
(rheMac2, Jan. 2006) produced by the Baylor College of Medicine Human
Genome Sequencing Center. For more information about these data, see the
Baylor web page at http://www.hgsc.bcm.tmc.edu/projects/rmacaque/.
Files included in this directory:
rheMac2.2bit - contains the complete rhesus/rheMac2 genome sequence
in the 2bit file format. 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. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
est.fa.gz - Rhesus macaque ESTs in GenBank. This sequence data is updated
once a week via automatic GenBank updates.
md5sum.txt - MD5 checksum of these files to verify correct transmission.
mrna.fa.gz - Rhesus macaque mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder are shown in
lower case; non-repeating sequence is shown in upper case.
RepeatMasker 19 Jan 2006 version with RepBase libraries: RepBase
Update 9.11, RM database version 20060120.
NOTE: In most assemblies, Tandem Repeats Finder repeats were
filtered to retain only the repeats with period <= 12. However,
the filtering was omitted for this assembly, so the lower case
masking includes all repeats.
chromFaMasked.tar.gz - The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns; non-repeating
sequence is shown in upper case.
chromOut.tar.gz - RepeatMasker .out file for chromosomes. These were
created by RepeatMasker at the -s sensitive setting.
chromTrf.tar.gz - Tandem Repeats Finder locations, translated into one
.bed file per chromosome.
NOTE: In most assemblies, Tandem Repeats Finder repeats were
filtered to retain only the repeats with period <= 12. However,
the filtering was omitted for this assembly, so these files contain
all Tandem Repeats Finder results.
rheMac2.agp.tar.gz - Description of how the assembly was generated from
fragments.
rheMac2.qual.qv.gz - base by base qual scores for rheMac2 assembly.
Values vary from 0 to 60.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the RefSeq data which is updated daily for most
assemblies.
upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
v1.edit3.noContam.ctg.fasta.gz - The unmasked contigs fasta from the assembly.
v1.edit3.noContam.ctg.qv.gz - The per base quality scores from contigs
sequences.
v1_edit4.scf.fasta.gz - The sequences for the large scaffolds that were
using in the assembly.
rheMac2.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/rheMac2/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Please review the restrictions on the use of the rhesus assembly data at
http://genome.ucsc.edu/goldenPath/credits.html#rhesus_use.
Name Last modified Size Description
Parent Directory -
chromFa.tar.gz 2006-06-12 15:13 832M
chromFaMasked.tar.gz 2006-06-12 15:20 457M
chromOut.tar.gz 2006-06-12 14:31 143M
chromTrf.tar.gz 2006-06-12 14:31 13M
est.fa.gz 2019-10-17 19:15 15M
est.fa.gz.md5 2019-10-17 19:15 44
md5sum.txt 2014-01-27 15:37 846
mrna.fa.gz 2019-10-17 19:00 139M
mrna.fa.gz.md5 2019-10-17 19:00 45
refMrna.fa.gz 2019-10-17 19:15 4.1M
refMrna.fa.gz.md5 2019-10-17 19:15 48
rheMac2.2bit 2006-01-30 18:00 712M
rheMac2.agp.tar.gz 2006-02-09 06:49 17M
rheMac2.chrom.sizes 2006-02-15 18:06 333
rheMac2.fa.gz 2020-01-23 02:25 833M
rheMac2.qual.qv.gz 2006-03-09 13:08 215M
upstream1000.fa.gz 2019-10-17 19:16 1.6M
upstream1000.fa.gz.md5 2019-10-17 19:16 53
upstream2000.fa.gz 2019-10-17 19:16 3.0M
upstream2000.fa.gz.md5 2019-10-17 19:16 53
upstream5000.fa.gz 2019-10-17 19:16 7.2M
upstream5000.fa.gz.md5 2019-10-17 19:16 53
v1.edit3.noContam.ctg.fasta.gz 2006-01-27 13:21 830M
v1.edit3.noContam.ctg.qv.gz 2006-01-27 13:23 287M
v1_edit4.scf.fasta.gz 2006-01-27 15:11 814M
xenoMrna.fa.gz 2019-10-17 19:10 6.6G
xenoMrna.fa.gz.md5 2019-10-17 19:11 49
xenoRefMrna.fa.gz 2019-10-17 19:15 327M
xenoRefMrna.fa.gz.md5 2019-10-17 19:15 52