{"id":168,"date":"2018-02-14T11:57:30","date_gmt":"2018-02-14T08:57:30","guid":{"rendered":"http:\/\/icg.nsc.ru\/plantgenomescollaboration\/?page_id=168"},"modified":"2019-10-31T08:11:38","modified_gmt":"2019-10-31T05:11:38","slug":"english-list-of-tools","status":"publish","type":"page","link":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/english-list-of-tools\/","title":{"rendered":"\u0421\u043f\u0438\u0441\u043e\u043a \u0438\u043d\u0441\u0442\u0440\u0443\u043c\u0435\u043d\u0442\u043e\u0432 \u0434\u043b\u044f \u0438\u0434\u0435\u043d\u0442\u0438\u0444\u0438\u043a\u0430\u0446\u0438\u0438 ncRNAs"},"content":{"rendered":"

\u0421\u043f\u0438\u0441\u043e\u043a \u043e\u0441\u043d\u043e\u0432\u043d\u044b\u0445 \u0438\u043d\u0441\u0442\u0440\u0443\u043c\u0435\u043d\u0442\u043e\u0432 \u0434\u043b\u044f \u0438\u0434\u0435\u043d\u0442\u0438\u0444\u0438\u043a\u0430\u0446\u0438\u0438 \u0438 \u0430\u043d\u043d\u043e\u0442\u0430\u0446\u0438\u0438 ncRNAs \u0443 \u0440\u0430\u0441\u0442\u0435\u043d\u0438\u0439<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
miRPlant<\/strong><\/td>\n\nIdentification of miRNAs from RNA-seq data
\nAn J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275.<\/p>\n

https:\/\/sourceforge.net\/projects\/mirplant\/<\/a>\n<\/td>\n<\/tr>\n

miRanalyzer<\/strong><\/td>\n\nIdentification of miRNAs and analysis of RNA-seq data (2017)https:\/\/sourceforge.net\/projects\/mirplant\/<\/p>\n

http:\/\/bioinfo5.ugr.es\/miRanalyzer\/miRanalyzer.php<\/a><\/p>\n<\/td>\n<\/tr>\n

miRA<\/strong><\/td>\n\nIdentification of miRNAs in organisms without existing miRNA annotation or without a known related organism with well-characterized miRNAs\tMichael Huttner (2016)<\/p>\n

https:\/\/github.com\/mhuttner\/miRA<\/a>\n<\/td>\n<\/tr>\n

miRDeep-P<\/strong><\/td>\n\nA modified miRDeep to predict plant miRNAs\t(2012)
\nhttp:\/\/faculty.virginia.edu\/lilab\/miRDP\/<\/a><\/p>\n<\/td>\n<\/tr>\n
Semirna<\/strong><\/td>\n\nIdentification of miRNAs using target sequences
\nhttp:\/\/www.bioinfocabd.upo.es\/semirna\/<\/a>\n<\/td>\n<\/tr>\n
TAPIR<\/strong><\/td>\n\nPrediction of miRNA targets, including target mimics
\nhttp:\/\/bioinformatics.psb.ugent.be\/webtools\/tapir\/<\/a><\/p>\n<\/td>\n<\/tr>\n
psRNATarget<\/strong><\/td>\n\nPrediction of miRNA targets, including reverse complementary matching and target site accessibility evaluation\t(2017)
\nhttp:\/\/plantgrn.noble.org\/psRNATarget\/<\/a><\/p>\n<\/td>\n<\/tr>\n
MicroPC<\/strong><\/td>\n\nIdentification of miRNAs and prediction of their targets from large-scale EST analysis\t(2009)
\nhttp:\/\/www3a.biotec.or.th\/micropc\/index.html <\/a><\/p>\n<\/td>\n<\/tr>\n
C-mii<\/strong><\/td>\n\nA software for Computational miRNA identification) Identification of miRNAs and prediction of their targets
\nhttp:\/\/www3a.biotec.or.th\/c-mii\/<\/a><\/p>\n<\/td>\n<\/tr>\n
MTide<\/strong><\/td>\n\nIdentification of miRNA\u202f\u2212\u202ftarget interaction by combining modified miRDeep2 and CleaveLand4 (2014)\tMing Chen’s Bioinformatics Group, Zhejiang University.
\nhttp:\/\/bis.zju.edu.cn\/MTide\/<\/a><\/p>\n<\/td>\n<\/tr>\n
BioVLAB-MMIA-NGS<\/strong><\/td>\n\n(MMIA= miRNA mRNA Integrated Analysis) Integrated analysis of miRNAs and mRNAs using high-throughput sequencing data
\nhttp:\/\/epigenomics.snu.ac.kr\/biovlab_mmia_ngs\/<\/a>\n<\/td>\n<\/tr>\n
PhlyoCSF<\/strong><\/td>\n\nCalculation of lncRNA coding potential using codon substitution frequency score
\nhttps:\/\/github.com\/mlin\/PhyloCSF<\/a><\/p>\n<\/td>\n<\/tr>\n
CPC<\/strong><\/td>\n\nCalculation of lncRNA coding potential using sequence features and support vector machine\t(2007-2015)
\nhttp:\/\/cpc.cbi.pku.edu.cn\/<\/a>\n<\/td>\n<\/tr>\n
CNCI<\/strong><\/td>\n\nCalculation of lncRNA coding potential by profiling adjoining nucleotide triplets
\nhttps:\/\/github.com\/www-bioinfo-org\/CNCI<\/a><\/p>\n<\/td>\n<\/tr>\n
CPAT<\/strong><\/td>\n\n(Coding Potential Assessment Tool) Calculation of lncRNA coding potential using a logistic regression model
\nhttp:\/\/rna-cpat.sourceforge.net\/<\/a>\n<\/td>\n<\/tr>\n
DeepLNC<\/strong><\/td>\n\nPrediction of lncRNAs using deep neural network
\nhttps:\/\/bioserver.iiita.ac.in\/deeplnc\/index.php<\/a>\n<\/td>\n<\/tr>\n
iSeeRNA<\/strong><\/td>\n\nPrediction of lncRNAs using support vector machine algorithm. CUHK\t(2014)<\/p>\n

http:\/\/137.189.133.71\/iSeeRNA\/<\/a>\n<\/td>\n<\/tr>\n

RegRNA<\/strong><\/td>\n\n\tIdentification of regulatory RNA motifs
\nhttp:\/\/regrna2.mbc.nctu.edu.tw\/index.html<\/a>\n<\/td>\n<\/tr>\n
spongeScan<\/strong><\/td>\n\nIdentification of miRNA sponges<\/p>\n

http:\/\/spongescan.rc.ufl.edu\/ <\/a>\n<\/td>\n<\/tr>\n<\/table>\n

<\/p>","protected":false},"excerpt":{"rendered":"

\u0421\u043f\u0438\u0441\u043e\u043a \u043e\u0441\u043d\u043e\u0432\u043d\u044b\u0445 \u0438\u043d\u0441\u0442\u0440\u0443\u043c\u0435\u043d\u0442\u043e\u0432 \u0434\u043b\u044f \u0438\u0434\u0435\u043d\u0442\u0438\u0444\u0438\u043a\u0430\u0446\u0438\u0438 \u0438 \u0430\u043d\u043d\u043e\u0442\u0430\u0446\u0438\u0438 ncRNAs \u0443 \u0440\u0430\u0441\u0442\u0435\u043d\u0438\u0439 miRPlant Identification of miRNAs from…<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/pages\/168"}],"collection":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/comments?post=168"}],"version-history":[{"count":1,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/pages\/168\/revisions"}],"predecessor-version":[{"id":275,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/pages\/168\/revisions\/275"}],"wp:attachment":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/wp-json\/wp\/v2\/media?parent=168"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}