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!
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:
ChrisL from the UCSC Genome Browser
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.
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.
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
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
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
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Thank you so much for your help!