博文
miRBase物种名缩写速查表 | 分享解决问题的过程，包治百病
|||
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：
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 |
| aae | Aedes aegypti |
| aau | Acacia auriculiformis |
| aca | Anolis carolinensis |
| aga | Anopheles gambiae |
| age | Ateles geoffroyi |
| ahy | Arachis hypogaea |
| aly | Arabidopsis lyrata |
| ame | Apis mellifera |
| amg | Acacia mangium |
| api | Acyrthosiphon pisum |
| aqc | Aquilegia caerulea |
| aqu | Amphimedon queenslandica |
| asu | Ascaris suum |
| ata | Aegilops tauschii |
| ath | Arabidopsis thaliana |
| bcy | Bruguiera cylindrica |
| bdi | Brachypodium distachyon |
| bfl | Branchiostoma floridae |
| bgy | Bruguiera gymnorhiza |
| bhv1 | Bovine herpesvirus 1 |
| bkv | BK polyomavirus |
| blv | Bovine leukemia virus |
| bma | Brugia malayi |
| bmo | Bombyx mori |
| bna | Brassica napus |
| bol | Brassica oleracea |
| bpcv1 | Bandicoot papillomatosis carcinomatosis virus type 1 |
| bpcv2 | Bandicoot papillomatosis carcinomatosis virus type 2 |
| bra | Brassica rapa |
| bta | Bos taurus |
| cbr | Caenorhabditis briggsae |
| cca | Cynara cardunculus |
| ccl | Citrus clementine |
| ccr | Cyprinus carpio |
| cel | Caenorhabditis elegans |
| cfa | Canis familiaris |
| cgr | Cricetulus griseus |
| cin | Ciona intestinalis |
| cla | Cerebratulus lacteus |
| cme | Cucumis melo |
| cpa | Carica papaya |
| cqu | Culex quinquefasciatus |
| cre | Chlamydomonas reinhardtii |
| crm | Caenorhabditis remanei |
| crt | Citrus reticulata |
| csa | Ciona savignyi |
| csi | Citrus sinensis |
| cte | Capitella teleta |
| ctr | Citrus trifoliata |
| dan | Drosophila ananassae |
| ddi | Dictyostelium discoideum |
| der | Drosophila erecta |
| dgr | Drosophila grimshawi |
| dme | Drosophila melanogaster |
| dmo | Drosophila mojavensis |
| dpe | Drosophila persimilis |
| dpr | Digitalis purpurea |
| dps | Drosophila pseudoobscura |
| dpu | Daphnia pulex |
| dre | Danio rerio |
| dse | Drosophila sechellia |
| dsi | Drosophila simulans |
| dvi | Drosophila virilis |
| dwi | Drosophila willistoni |
| dya | Drosophila yakuba |
| ebv | Epstein Barr virus |
| eca | Equus caballus |
| egr | Echinococcus granulosus |
| egu | Elaeis guineensis |
| emu | Echinococcus multilocularis |
| esi | Ectocarpus siliculosus |
| far | Festuca arundinacea |
| fru | Fugu rubripes |
| gar | Gossypium arboreum |
| gga | Gallus gallus |
| ggo | Gorilla gorilla |
| ghb | Gossypium herbaceum |
| ghr | Gossypium hirsutum |
| gma | Glycine max |
| gpy | Glottidia pyramidata |
| gra | Gossypium raimondii |
| gso | Glycine soja |
| han | Helianthus annuus |
| har | Helianthus argophyllus |
| hbr | Hevea brasiliensis |
| hbv | Herpes B virus |
| hci | Helianthus ciliaris |
| hcmv | Human cytomegalovirus |
| hco | Haemonchus contortus |
| hex | Helianthus exilis |
| hhi | Hippoglossus hippoglossus |
| hhv6b | Human herpesvirus 6B |
| hiv1 | Human immunodeficiency virus 1 |
| hma | Hydra magnipapillata |
| hme | Heliconius melpomene |
| hpa | Helianthus paradoxus |
| hpe | Helianthus petiolaris |
| hru | Haliotis rufescens |
| hsa | Homo sapiens |
| hsv1 | Herpes Simplex Virus 1 |
| hsv2 | Herpes Simplex Virus 2 |
| htu | Helianthus tuberosus |
| hvsa | Herpesvirus saimiri strain A11 |
| hvt | Herpesvirus of turkeys |
| hvu | Hordeum vulgare |
| iltv | Infectious laryngotracheitis virus |
| isc | Ixodes scapularis |
| jcv | JC polyomavirus |
| kshv | Kaposi sarcoma-associated herpesvirus |
| lca | Lemur catta |
| lgi | Lottia gigantea |
| lja | Lotus japonicus |
| lla | Lagothrix lagotricha |
| lmi | Locusta migratoria |
| mcmv | Mouse cytomegalovirus |
| mcv | Merkel cell polyomavirus |
| mdm | Malus domestica |
| mdo | Monodelphis domestica |
| mdv1 | Mareks disease virus |
| mdv2 | Mareks disease virus type 2 |
| mes | Manihot esculenta |
| meu | Macropus eugenii |
| mghv | Mouse gammaherpesvirus 68 |
| mja | Marsupenaeus japonicus |
| mml | Macaca mulatta |
| mmu | Mus musculus |
| mne | Macaca nemestrina |
| mse | Manduca sexta |
| mtr | Medicago truncatula |
| ngi | Nasonia giraulti |
| nlo | Nasonia longicornis |
| nta | Nicotiana tabacum |
| nve | Nematostella vectensis |
| nvi | Nasonia vitripennis |
| oan | Ornithorhynchus anatinus |
| oar | Ovis aries |
| odi | Oikopleura dioica |
| ola | Oryzias latipes |
| osa | Oryza sativa |
| pab | Picea abies |
| pbi | Pygathrix bieti |
| pde | Pinus densata |
| peu | Populus euphratica |
| pma | Petromyzon marinus |
| pol | Paralichthys olivaceus |
| ppa | Pan paniscus |
| ppc | Pristionchus pacificus |
| ppt | Physcomitrella patens |
| ppy | Pongo pygmaeus |
| prv | Pseudorabies virus |
| pta | Pinus taeda |
| ptc | Populus trichocarpa |
| pti | Phaeodactylum tricornutum |
| ptr | Pan troglodytes |
| pvu | Phaseolus vulgaris |
| rco | Ricinus communis |
| rgl | Rehmannia glutinosa |
| rlcv | Rhesus lymphocryptovirus |
| rmi | Rhipicephalus microplus |
| rno | Rattus norvegicus |
| rrv | Rhesus monkey rhadinovirus |
| sbi | Sorghum bicolor |
| sha | Sarcophilus harrisii |
| sja | Schistosoma japonicum |
| sko | Saccoglossus kowalevskii |
| sla | Saguinus labiatus |
| sly | Solanum lycopersicum |
| sma | Schistosoma mansoni |
| sme | Schmidtea mediterranea |
| smo | Selaginella moellendorffii |
| smr | Strigamia maritima |
| sof | Saccharum officinarum |
| spu | Strongylocentrotus purpuratus |
| ssc | Sus scrofa |
| ssl | Salvia sclarea |
| ssp | Saccharum ssp. |
| ssy | Symphalangus syndactylus |
| stu | Solanum tuberosum |
| sv40 | Simian virus 40 |
| tae | Triticum aestivum |
| tca | Tribolium castaneum |
| tcc | Theobroma cacao |
| tgu | Taeniopygia guttata |
| tni | Tetraodon nigroviridis |
| tre | Terebratulina retusa |
| ttu | Triticum turgidum |
| tur | Tetranychus urticae |
| vun | Vigna unguiculata |
| vvi | Vitis vinifera |
| xbo | Xenoturbella bocki |
| xla | Xenopus laevis |
| xtr | Xenopus tropicalis |
| zma | Zea 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
miRNA相关：
其他速查表
https://blog.sciencenet.cn/blog-3372875-1090490.html
上一篇：水生生物的ATAC-seq数据和文章都在这里
下一篇：Ensembl基因组+注释 | 物种速查 | 植物
