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Question: Get UCSC Genome Browser assembly ID
1
gravatar for uxue33
6 months ago by
uxue33 • 20
uxue33 • 20 wrote:

Hello all,

I'm beginning to work with data bases form my Master Thesis.

I want to map each organism name with the corresponding UCSC Genome Browser assembly ID to save it in a table. As I don't have the UCSC database available to work with MySQL my question is if there is any way to get all the UCSC Genome Browser assembly ID.

Thanks you all!
assembly • 352 views
ADD COMMENT • link •
modified 6 months ago by genecats.ucsc • 560 • written 6 months ago by uxue33 • 20
1
gravatar for genecats.ucsc
6 months ago by
genecats.ucsc • 560
genecats.ucsc • 560 wrote:

Genomax already answered, but here is also a mysql command you can use if you don't want to download the entire hgcentral database dump:

$ mysql -h genome-mysql.soe.ucsc.edu -u genome -e "select name, scientificName from dbDb limit 5" hgcentral
+---------+-------------------------------------+
| name    | scientificName                      |
+---------+-------------------------------------+
| hg38    | Homo sapiens                        |
| balAcu1 | Balaenoptera acutorostrata scammoni |
| calMil1 | Callorhinchus milii                 |
| rn6     | Rattus norvegicus                   |
| sorAra2 | Sorex araneus                       |
+---------+-------------------------------------+

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

  • General questions: genome@soe.ucsc.edu
  • Questions involving private data: genome-www@soe.ucsc.edu
  • Questions involving mirror sites: genome-mirror@ose.ucsc.edu

ChrisL from the UCSC Genome Browser
ADD COMMENT • link written 6 months ago by genecats.ucsc • 560

Thank you so much for your help!

ADD REPLY • link written 6 months ago by uxue33 • 20
2
gravatar for genomax
6 months ago by
genomax ♦ 55k
United States
genomax ♦ 55k wrote:

You can use the public MySQL server made available by UCSC to query any data you need.

That said UCSC only has a subset of genomes available.
ADD COMMENT • link written 6 months ago by genomax ♦ 55k

Thank you for your answer but I still can not guess how to obtain a list with the species name and the corresponding UCSC Genome Browser assembly ID.

ADD REPLY • link written 6 months ago by uxue33 • 20
1

Not exactly sure what you mean by Genome Browser Assembly ID but if you look in this directory of all genomes every folder should have a bigZips folder. There are .2bit genome files in these folders that have the assembly name (If that is what you mean by ID). e.g. In this folder, anoGam1.2bit for Mosquito.

UCSC uses the same genome build ID's as used by entities that release official genome builds for various organisms.

ADD REPLY • link modified 6 months ago • written 6 months ago by genomax ♦ 55k

What I'm looking is to pair for example Homo sapiens with hg38 (which is the UCSC Genome Browser assembly ID), I don't need any information about the genome itself.

Thank you for your answers!

ADD REPLY • link written 6 months ago by uxue33 • 20

Have to split into three posts. 

 hg38            Human
    balAcu1         Minke whale
    calMil1         Elephant shark
    rn6             Rat
    sorAra2         Shrew
    taeGut2         Zebra finch
    takFla1         Yellowbelly pufferfish
    tupChi1         Chinese tree shrew
    pteAle1         Black flying-fox
    punNye1         Pundamilia nyererei
    vicPac2         Alpaca
    hg38Patch3              GRCh38.p3
    felCat8         Cat
    amaVit1         Parrot
    anaPla1         Mallard duck
    apaSpi1         Spiny softshell turtle
    araMac1         Scarlet macaw
    astMex1         Mexican tetra (cavefish)
    camFer1         Bactrian camel
    capHir1         Domestic goat
    cheMyd1         Green seaturtle
    chiLan1         Chinchilla
    chlSab1         Green monkey
    chrAsi1         Cape golden mole
    colLiv1         Rock pigeon
    conCri1         Star-nosed mole
    criGri1         Chinese hamster
    eleEdw1         Cape elephant shrew
    eptFus1         Big brown bat
    eriEur2         Hedgehog
    falChe1         Saker falcon
    falPer1         Peregrine falcon
    ficAlb2         Collared flycatcher
    hapBur1         Burton\
    jacJac1         Lesser Egyptian jerboa
    lepOcu1         Spotted gar
    lepWed1         Weddell seal
    macFas5         Crab-eating macaque
    mayZeb1         Zebra mbuna
    mesAur1         Golden hamster
    micOch1         Prairie vole
    myoDav1         David\
    neoBri1         Princess of Burundi
    ochPri3         Pika
    octDeg1         Brush-tailed rat
    odoRosDiv1              Pacific walrus
    papAnu2         Baboon
    cerSim1         White rhinoceros
    nomLeu3         Gibbon
    musFur1         Ferret 
    allMis1         American alligator
    echTel2         Tenrec
    oviAri3         Sheep
    bosTau7         Cow
    chrPic1         Painted turtle
    galGal4         Chicken
    rn5             Rat
    canFam3         Dog
    sarHar1         Tasmanian devil
    speTri2         Squirrel
    melUnd1         Budgerigar
    otoGar3         Bushbaby
    rheMac3         Rhesus
    panTro4         Chimp
    saiBol1         Squirrel monkey
    triMan1         Manatee
    oreNil2         Nile tilapia
    turTru2         Dolphin
    dasNov3         Armadillo
    felCat5         Cat
    susScr3         Pig
    hetGla2         Naked mole-rat
    nomLeu2         Gibbon
    hg19Patch9              Grch37.p9
    geoFor1         Medium ground finch
    dm6             D. melanogaster
    mm10Patch1              Grcm38.p1
    braFlo2         Lancelet
    felCat4         Cat
    bosTau5         Cow
    hg19Patch2              GRCh37.p2
    danRer7         Zebrafish
    panTro3         Chimp
    oviAri1         Sheep
    anoCar2         Lizard
    hg19Patch5              Grch37.p5
    sacCer3         S. cerevisiae
    bosTau6         Cow
    xenTro3         X. tropicalis
    melGal1         Turkey
    myoLuc2         Microbat
    gorGor3         Gorilla
    nomLeu1         Gibbon
    ce10            C. elegans
    macEug2         Wallaby
    mm10            Mouse
    fr3             Fugu
    hetGla1         Naked mole-rat
    oreNil1         Nile tilapia
    gadMor1         Atlantic cod
    musDom2         M. domestica
    orcOrc1         Killer whale
    xenTro7         X. tropicalis
    xipMac1         Southern platyfish
    oryAfe1         Aardvark
    hg19Patch10             Grch37.p10
    zonAlb1         White-throated sparrow
    latCha1         Coelacanth
    eboVir3         Ebola virus
    panHod1         Tibetan antelope
    pelSin1         Chinese softshell turtle
    pseHum1         Tibetan ground jay
    apiMel4         A. mellifera
    calJac3         Marmoset
    micMur1         Mouse lemur
    petMar1         Lamprey
    droWil1         D. willistoni
    dp4             D. pseudoobscura
    felCat3         Cat
    bosTau3         Cow
    ce11            C. elegans
    aptMan1         Brown kiwi
    equCab2         Horse
    turTru1         Dolphin
    droEre2         D. erecta
    macEug1         Wallaby
    galGal2         Chicken
    hg15            Human
    chrPic2         Painted turtle
    fr1             Fugu
    droBip2         D. bipectinata
ADD REPLY • link modified 6 months ago • written 6 months ago by genomax ♦ 55k 
cb1             C. briggsae
    sacCer1         S. cerevisiae
    panTro1         Chimp
    hg16            Human
    rn3             Rat
    dm1             D. melanogaster
    cavPor3         Guinea pig
    mm6             Mouse
    ce2             C. elegans
    danRer2         Zebrafish
    droEre1         D. erecta
    monDom1         Opossum
    apiMel1         A. mellifera
    dp3             D. pseudoobscura
    droVir1         D. virilis
    droMoj1         D. mojavensis
    xenTro1         X. tropicalis
    droAna1         D. ananassae
    dm2             D. melanogaster
    droBia2         D. biarmipes
    hg17            Human
    droYak1         D. yakuba
    echTel1         Tenrec
    droGri1         D. grimshawi
    anoGam1         A. gambiae
    danRer1         Zebrafish
    ci1             C. intestinalis
    droPse3         D. pseudoobscura
    canFam1         Dog
    dp2             D. pseudoobscura
    tetNig1         Tetraodon
    mm10Patch4              GRCm38.p4
    taeGut1         Zebra finch
    apiMel2         A. mellifera
    droMoj2         D. mojavensis
    droAna2         D. ananassae
    bosTau2         Cow
    ci2             C. intestinalis
    bosTau1         Cow
    rheMac1         Rhesus
    tarSyr2         Tarsier
    caePb2          C. brenneri
    droSim1         D. simulans
    strPur1         S. purpuratus
    canFam2         Dog
    droEug2         D. eugracilis
    oryCun1         Rabbit
    danRer3         Zebrafish
    dasNov1         Armadillo
    loxAfr1         Elephant
    triCas1         T. castaneum
    ce6             C. elegans
    droVir2         D. virilis
    monDom2         Opossum
    mm7             Mouse
    droEle2         D. elegans
    bosTau4         Cow
    gorGor5         Gorilla
    hg18            Human
    monDom5         Opossum
    rn4             Rat
    danRer5         Zebrafish
    droYak2         D. yakuba
    hg38Patch2              GRCh38.p2
    triCas2         T. castaneum
    droPer1         D. persimilis
    droSec1         D. sechellia
    droSuz1         D. suzukii
    caeJap1         C. japonica
    hg38Patch9              GRCh38.p9
    rheMac2         Rhesus
    choHof1         Sloth
    monDom4         Opossum
    panTro2         Chimp
    mm8             Mouse
    danRer4         Zebrafish
    xenTro2         X. tropicalis
    galGal3         Chicken
    panPan1         Bonobo
    rhiRox1         Golden snub-nosed monkey
    nasLar1         Proboscis monkey
    chlSab2         Green monkey
    micMur2         Mouse lemur
    bosTau8         Cow
    droVir3         D. virilis
    gasAcu1         Stickleback
    droAna3         D. ananassae
    dm3             D. melanogaster
    droMoj3         D. mojavensis
    droGri2         D. grimshawi
    oryLat1         Medaka
    otoGar1         Bushbaby
    ornAna1         Platypus
    tupBel1         Tree shrew
    fr2             Fugu
    braFlo1         Lancelet
    equCab1         Horse
    anoCar1         Lizard
    caePb1          C. brenneri
    priPac1         P. pacificus
    ce4             C. elegans
    cb3             C. briggsae
    strPur2         S. purpuratus
    sorAra1         Shrew
    caeRem2         C. remanei
    cavPor2         Guinea pig
    vicPac1         Alpaca
    gorGor1         Gorilla
    tarSyr1         Tarsier
    ponAbe2         Orangutan
    calJac1         Marmoset
    eriEur1         Hedgehog
    mm9             Mouse
    caeRem3         C. remanei
    ornAna2         Platypus
    hg38Patch6              GRCh38.p6
    pteVam1         Megabat
    apiMel3         A. mellifera
    dipOrd1         Kangaroo rat
    proCap1         Rock hyrax
ADD REPLY • link written 6 months ago by genomax ♦ 55k 
ochPri2         Pika
myoLuc1         Microbat
droAlb1         D. albomicans
loxAfr2         Elephant
dasNov2         Armadillo
speTri1         Squirrel
oryLat2         Medaka
galVar1         Malayan flying lemur
sacCer2         S. cerevisiae
hg19            Human
rheMac8         Rhesus
gorGor4         Gorilla
hg38Patch7              GRCh38.p7
aplCal1         Sea hare
papHam1         Baboon
petMar2         Lamprey
danRer6         Zebrafish
loxAfr3         Elephant
droTak2         D. takahashii
droKik2         D. kikkawai
droYak3         D. yakuba
droWil2         D. willistoni
droMir2         D. miranda
droFic2         D. ficusphila
droRho2         D. rhopaloa
tetNig2         Tetraodon
oryCun2         Rabbit
galGal5         Chicken
bosTauMd3               Cow
ailMel1         Panda
danRer10                Zebrafish
susScr2         Pig
panTro5         Chimp
melGal5         Turkey
bisBis1         Bison
nanPar1         Tibetan frog
manPen1         Chinese pangolin
aquChr2         Golden eagle
ci3             C. intestinalis
hg38Patch11             GRCh38.p11
danRer11                Zebrafish
criGriChoV1             Chinese hamster
susScr11                Pig
xenLae2         African clawed frog
xenTro9         X. tropicalis
panPan2         Bonobo
ADD REPLY • link written 6 months ago by genomax ♦ 55k

Thanks a lot for this work! How have you done it? Is there anywhere I can download it?

Thanks again!

ADD REPLY • link written 6 months ago by uxue33 • 20
2

The information is in hgcentral MySQL dump file.

ADD REPLY • link written 6 months ago by genomax ♦ 55k
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