This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/mm39/multiz35way/README.txt
This directory contains compressed multiple alignments of
34 genomes to the mouse/mm39/Jun. 2020 genome.
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm39&g=cons35way
based on the phylogenetic tree: mm39.35way.nh.
mm39.35way.maf.gz
Files in this directory:
- mm39.35way.nh - phylogenetic tree used during the multiz multiple
alignment, using the UCSC database name, or sequence name for those
sequences that are not hosted in UCSC databases.
- mm39.35way.scientificName.nh - same as mm39.35way.nh with the
sequence name replaced with the scientific name for the species.
- mm39.35way.commonNames.nh - same as mm39.35way.nh with the sequence
name replaced with the common name
- mm39.35way.maf.gz - multiple alignments on zebrafish
- upstream*.ensGene.maf.gz - alignments of regions upstream of
Ensembl genes
- md5sum.txt - md5 check sums of these files to verify correct download files
The "alignments" directory contains compressed FASTA alignments
for the CDS regions for the gene track: NCBI RefSeq,
of the Chinese hamster genome
(GCF_0003668045.3 CriGri-PICRH-1, Jun. 2020) aligned to the assemblies.
The mm39.35way.maf.gz file contains all the alignments on the zebrafish
genome, including additional annotations to indicate gap
context and genomic breaks for the sequence in the underlying
genome assemblies. Note, the compressed data size of these
maf files is 3 Gb, uncompressed is approximately 20 Gb.
The upstream*.ensGene.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl genes. with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in
chicken, whether or not alignments actually exist. In situations where no
alignments exist or the alignments of one or more species are missing,
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in chicken; therefore, only the
species name is displayed in the alignment data and no position information
is recorded. The alignment score is always zero in these files.
For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.
PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm39/phastCons35way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm39/phyloP35way
---------------------------------------------------------------
Assemblies used in these alignments:
Mouse - Mus musculus
Jun. 2020 (GRCm39/mm39) (reference)
Beaver - Castor canadensis
Feb. 2017 (C.can genome v1.0/casCan1) (reciprocal best)
Bonobo - Pan paniscus
May 2020 (Mhudiblu_PPA_v0/panPan3) (syntenic)
Bushbaby - Otolemur garnettii
Mar. 2011 (Broad/otoGar3) (reciprocal best)
Chicken - Gallus gallus
Mar. 2018 (GRCg6a/galGal6) (maf net)
Chimp - Pan troglodytes
Jan. 2018 (Clint_PTRv2/panTro6) (syntenic)
Chinese hamster - Cricetulus griseus
Jun. 2020 (GCF_0003668045.3 CriGri-PICRH-1.0) (syntenic)
Chinese pangolin - Manis pentadactyla
Aug 2014 (M_pentadactyla-1.1.1/manPen1) (reciprocal best)
Cow - Bos taurus
Apr. 2018 (ARS-UCD1.2/bosTau9) (reciprocal best)
Dog - Canis lupus familiaris
Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) (syntenic)
Dolphin - Tursiops truncatus
Oct. 2011 (Baylor Ttru_1.4/turTru2) (reciprocal best)
Elephant - Loxodonta africana
Jul. 2009 (Broad/loxAfr3) (reciprocal best)
Gorilla - Gorilla gorilla gorilla
Aug. 2019 (Kamilah_GGO_v0/gorGor6) (syntenic)
Guinea pig - Cavia porcellus
Feb. 2008 (Broad/cavPor3) (syntenic)
Hawaiian monk seal - Neomonachus schauinslandi
Jun. 2017 (ASM220157v1/neoSch1) (syntenic)
Hedgehog - Erinaceus europaeus
May 2012 (EriEur2.0/eriEur2) (reciprocal best)
Horse - Equus caballus
Jan. 2018 (EquCab3.0/equCab3) (syntenic)
Human - Homo sapiens
Dec. 2013 (GRCh38/hg38) (syntenic)
Lamprey - Petromyzon marinus
Dec. 2017 (Pmar_germline 1.0/petMar3) (maf net)
Malayan flying lemur - Galeopterus variegatus
Jun. 2014 (G_variegatus-3.0.2/galVar1) (maf net)
Marmoset - Callithrix jacchus
May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4) (syntenic)
Opossum - Monodelphis domestica
Oct. 2006 (Broad/monDom5) (maf net)
Pig - Sus scrofa
Aug. 2011 (SGSC Sscrofa10.2/susScr3) (reciprocal best)
Pika - Ochotona princeps
May 2012 (OchPri3.0/ochPri3) (reciprocal best)
Rabbit - Oryctolagus cuniculus
Apr. 2009 (Broad/oryCun2) (reciprocal best)
Rat - Rattus norvegicus
Jul. 2014 (RGSC 6.0/rn6) (syntenic)
Rhesus - Macaca mulatta
Feb. 2019 (Mmul_10/rheMac10) (syntenic)
Sheep - Ovis aries
Nov. 2015 (Oar_v4.0/oviAri4) (syntenic)
Shrew - Sorex araneus
Aug. 2008 (Broad/sorAra2) (reciprocal best)
Squirrel - Spermophilus tridecemlineatus
Nov. 2011 (Broad/speTri2) (reciprocal best)
Tarsier - Tarsius syrichta
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) (reciprocal best)
Tenrec - Echinops telfairi
Nov. 2012 (Broad/echTel2) (reciprocal best)
Tree shrew - Tupaia belangeri
Dec. 2006 (Broad/tupBel1) (reciprocal best)
X. tropicalis - Xenopus tropicalis
Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) (maf net)
Zebrafish - Danio rerio
May 2017 (GRCz11/danRer11) (maf net)
---------------------------------------------------------------
To download a large file or multiple files from this directory, we recommend
that you use rsync or ftp rather than downloading the files via our website.
There is approximately 20 Gb of compressed data in this directory,
approximately 170 Gb uncompressed.
Via rsync:
rsync -av --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/mm39/multiz35way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/mm39/multiz35way
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Use the "prompt" command to toggle the interactive mode if you do not want
to be prompted for each file that you download.
---------------------------------------------------------------
All the files in this directory are freely usable for any
purpose. For data use restrictions regarding the individual
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.
Name Last modified Size Description
Parent Directory -
alignments/ 2021-08-30 15:03 -
maf/ 2021-01-27 15:44 -
md5sum.txt 2021-01-11 15:29 366
mm39.35way.nh 2020-12-23 14:56 1.3K
mm39.35way.commonNames.nh 2020-12-23 14:59 1.3K
mm39.35way.scientificNames.nh 2020-12-23 15:00 1.6K
upstream300.ncbiRefSeq.maf.gz 2021-01-04 17:04 92M
upstream2000.ncbiRefSeq.maf.gz 2021-01-04 17:41 904M
upstream5000.ncbiRefSeq.maf.gz 2021-01-04 18:48 1.9G