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miRBase物种名缩写速查表 | 分享解决问题的过程,包治百病

已有 17878 次阅读 2017-12-19 12:56 |个人分类:物种速查|系统分类:科研笔记| 物种名

 

本文转载自嘉因微信公众号,已获得授权。查看最新文章,敬请关注嘉因,微信ID:rainbow-genome

作者:小哈  来源:嘉因

先吐槽!最近做非模式生物的项目,miRBase一点也不友好,我只能猜出人和小鼠,其他的缩写都是什么鬼?去哪找缩写跟物种名字对应的list?


打开微信,搜一搜,还真搜到了一篇:

》》》miRNA的命名规则详解以及最全物种三字母缩写表


这里有个缩写-拉丁名-中文名的图片,没错,就是图片。缩写没按字母排序,找得我眼花缭乱。


罢了,不敢偷懒了,自己搞。




小哈喜欢授人以渔,把过程分享出来。下面这些操作,生信盲在Window系统下就能搞定。有人说R算不上编程语言,它就是一个隐身的Excel表格。很多问题都能找到相应的R包来解决。


包治百病!


miRBase有个包——mirbase.db,前天刚更新了说明文档。


谁说我闲的老是检查更新?还有更闲的在这儿呢!

》》》掐架的额外收获(此处有链接,17个R包作者的公众号)


在R里输入下面两行,安装mirbase.db包

source("https://bioconductor.org/biocLite.R")

biocLite("mirbase.db")


然后输入下面这两行

library(mirbase.db)

write.table(toTable(mirbaseSPECIES),file = "organism.txt",quote = F,sep = "\t")


就输出了这样的列表,跟上面提到的图片里的顺序是一样的。第二列是三个字母的缩写,第三列是学名。


排个序,这样就好找了。

缩写拉丁名
aaeAedes aegypti
aauAcacia auriculiformis
acaAnolis carolinensis
agaAnopheles gambiae
ageAteles geoffroyi
ahyArachis hypogaea
alyArabidopsis lyrata
ameApis mellifera
amgAcacia mangium
apiAcyrthosiphon pisum
aqcAquilegia caerulea
aquAmphimedon queenslandica
asuAscaris suum
ataAegilops tauschii
athArabidopsis thaliana
bcyBruguiera cylindrica
bdiBrachypodium distachyon
bflBranchiostoma floridae
bgyBruguiera gymnorhiza
bhv1Bovine herpesvirus 1
bkvBK polyomavirus
blvBovine leukemia virus
bmaBrugia malayi
bmoBombyx mori
bnaBrassica napus
bolBrassica oleracea
bpcv1Bandicoot papillomatosis carcinomatosis virus type 1
bpcv2Bandicoot papillomatosis carcinomatosis virus type 2
braBrassica rapa
btaBos taurus
cbrCaenorhabditis briggsae
ccaCynara cardunculus
cclCitrus clementine
ccrCyprinus carpio
celCaenorhabditis elegans
cfaCanis familiaris
cgrCricetulus griseus
cinCiona intestinalis
claCerebratulus lacteus
cmeCucumis melo
cpaCarica papaya
cquCulex quinquefasciatus
creChlamydomonas reinhardtii
crmCaenorhabditis remanei
crtCitrus reticulata
csaCiona savignyi
csiCitrus sinensis
cteCapitella teleta
ctrCitrus trifoliata
danDrosophila ananassae
ddiDictyostelium discoideum
derDrosophila erecta
dgrDrosophila grimshawi
dmeDrosophila melanogaster
dmoDrosophila mojavensis
dpeDrosophila persimilis
dprDigitalis purpurea
dpsDrosophila pseudoobscura
dpuDaphnia pulex
dreDanio rerio
dseDrosophila sechellia
dsiDrosophila simulans
dviDrosophila virilis
dwiDrosophila willistoni
dyaDrosophila yakuba
ebvEpstein Barr virus
ecaEquus caballus
egrEchinococcus granulosus
eguElaeis guineensis
emuEchinococcus multilocularis
esiEctocarpus siliculosus
farFestuca arundinacea
fruFugu rubripes
garGossypium arboreum
ggaGallus gallus
ggoGorilla gorilla
ghbGossypium herbaceum
ghrGossypium hirsutum
gmaGlycine max
gpyGlottidia pyramidata
graGossypium raimondii
gsoGlycine soja
hanHelianthus annuus
harHelianthus argophyllus
hbrHevea brasiliensis
hbvHerpes B virus
hciHelianthus ciliaris
hcmvHuman cytomegalovirus
hcoHaemonchus contortus
hexHelianthus exilis
hhiHippoglossus hippoglossus
hhv6bHuman herpesvirus 6B
hiv1Human immunodeficiency virus 1
hmaHydra magnipapillata
hmeHeliconius melpomene
hpaHelianthus paradoxus
hpeHelianthus petiolaris
hruHaliotis rufescens
hsaHomo sapiens
hsv1Herpes Simplex Virus 1
hsv2Herpes Simplex Virus 2
htuHelianthus tuberosus
hvsaHerpesvirus saimiri strain A11
hvtHerpesvirus of turkeys
hvuHordeum vulgare
iltvInfectious laryngotracheitis virus
iscIxodes scapularis
jcvJC polyomavirus
kshvKaposi sarcoma-associated herpesvirus
lcaLemur catta
lgiLottia gigantea
ljaLotus japonicus
llaLagothrix lagotricha
lmiLocusta migratoria
mcmvMouse cytomegalovirus
mcvMerkel cell polyomavirus
mdmMalus domestica
mdoMonodelphis domestica
mdv1Mareks disease virus
mdv2Mareks disease virus type 2
mesManihot esculenta
meuMacropus eugenii
mghvMouse gammaherpesvirus 68
mjaMarsupenaeus japonicus
mmlMacaca mulatta
mmuMus musculus
mneMacaca nemestrina
mseManduca sexta
mtrMedicago truncatula
ngiNasonia giraulti
nloNasonia longicornis
ntaNicotiana tabacum
nveNematostella vectensis
nviNasonia vitripennis
oanOrnithorhynchus anatinus
oarOvis aries
odiOikopleura dioica
olaOryzias latipes
osaOryza sativa
pabPicea abies
pbiPygathrix bieti
pdePinus densata
peuPopulus euphratica
pmaPetromyzon marinus
polParalichthys olivaceus
ppaPan paniscus
ppcPristionchus pacificus
pptPhyscomitrella patens
ppyPongo pygmaeus
prvPseudorabies virus
ptaPinus taeda
ptcPopulus trichocarpa
ptiPhaeodactylum tricornutum
ptrPan troglodytes
pvuPhaseolus vulgaris
rcoRicinus communis
rglRehmannia glutinosa
rlcvRhesus lymphocryptovirus
rmiRhipicephalus microplus
rnoRattus norvegicus
rrvRhesus monkey rhadinovirus
sbiSorghum bicolor
shaSarcophilus harrisii
sjaSchistosoma japonicum
skoSaccoglossus kowalevskii
slaSaguinus labiatus
slySolanum lycopersicum
smaSchistosoma mansoni
smeSchmidtea mediterranea
smoSelaginella moellendorffii
smrStrigamia maritima
sofSaccharum officinarum
spuStrongylocentrotus purpuratus
sscSus scrofa
sslSalvia sclarea
sspSaccharum ssp.
ssySymphalangus syndactylus
stuSolanum tuberosum
sv40Simian virus 40
taeTriticum aestivum
tcaTribolium castaneum
tccTheobroma cacao
tguTaeniopygia guttata
tniTetraodon nigroviridis
treTerebratulina retusa
ttuTriticum turgidum
turTetranychus urticae
vunVigna unguiculata
vviVitis vinifera
xboXenoturbella bocki
xlaXenopus laevis
xtrXenopus tropicalis
zmaZea mays


延伸阅读:不懂生信,不装Linux,也能Run代码—Windows系统的Linux命令行工具Babun



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