{"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\/en\/english-list-of-tools\/","title":{"rendered":"List of tools for identifying and annotating ncRNAs in plants"},"content":{"rendered":"

List of key tools for identifying and annotating ncRNAs in plants<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
miRPlant<\/strong><\/td>\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.https:\/\/sourceforge.net\/projects\/mirplant\/<\/a><\/td>\n<\/tr>\n
miRanalyzer<\/strong><\/td>\nIdentification of miRNAs and analysis of RNA-seq data (2017)https:\/\/sourceforge.net\/projects\/mirplant\/http:\/\/bioinfo5.ugr.es\/miRanalyzer\/miRanalyzer.php<\/a><\/td>\n<\/tr>\n
miRA<\/strong><\/td>\nIdentification of miRNAs in organisms without existing miRNA annotation or without a known related organism with well-characterized miRNAs Michael Huttner (2016)https:\/\/github.com\/mhuttner\/miRA<\/a><\/td>\n<\/tr>\n
miRDeep-P<\/strong><\/td>\nA modified miRDeep to predict plant miRNAs (2012)
\nhttp:\/\/faculty.virginia.edu\/lilab\/miRDP\/<\/a><\/td>\n<\/tr>\n
Semirna<\/strong><\/td>\nIdentification of miRNAs using target sequences
\nhttp:\/\/www.bioinfocabd.upo.es\/semirna\/<\/a><\/td>\n<\/tr>\n
TAPIR<\/strong><\/td>\nPrediction of miRNA targets, including target mimics
\nhttp:\/\/bioinformatics.psb.ugent.be\/webtools\/tapir\/<\/a><\/td>\n<\/tr>\n
psRNATarget<\/strong><\/td>\nPrediction of miRNA targets, including reverse complementary matching and target site accessibility evaluation (2017)
\nhttp:\/\/plantgrn.noble.org\/psRNATarget\/<\/a><\/td>\n<\/tr>\n
MicroPC<\/strong><\/td>\nIdentification of miRNAs and prediction of their targets from large-scale EST analysis (2009)
\nhttp:\/\/www3a.biotec.or.th\/micropc\/index.html <\/a><\/td>\n<\/tr>\n
C-mii<\/strong><\/td>\nA software for Computational miRNA identification) Identification of miRNAs and prediction of their targets
\nhttp:\/\/www3a.biotec.or.th\/c-mii\/<\/a><\/td>\n<\/tr>\n
MTide<\/strong><\/td>\nIdentification of miRNA\u202f\u2212\u202ftarget interaction by combining modified miRDeep2 and CleaveLand4 (2014) Ming Chen’s Bioinformatics Group, Zhejiang University.
\nhttp:\/\/bis.zju.edu.cn\/MTide\/<\/a><\/td>\n<\/tr>\n
BioVLAB-MMIA-NGS<\/strong><\/td>\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><\/td>\n<\/tr>\n
PhlyoCSF<\/strong><\/td>\nCalculation of lncRNA coding potential using codon substitution frequency score
\nhttps:\/\/github.com\/mlin\/PhyloCSF<\/a><\/td>\n<\/tr>\n
CPC<\/strong><\/td>\nCalculation of lncRNA coding potential using sequence features and support vector machine (2007-2015)
\nhttp:\/\/cpc.cbi.pku.edu.cn\/<\/a><\/td>\n<\/tr>\n
CNCI<\/strong><\/td>\nCalculation of lncRNA coding potential by profiling adjoining nucleotide triplets
\nhttps:\/\/github.com\/www-bioinfo-org\/CNCI<\/a><\/td>\n<\/tr>\n
CPAT<\/strong><\/td>\n(Coding Potential Assessment Tool) Calculation of lncRNA coding potential using a logistic regression model
\nhttp:\/\/rna-cpat.sourceforge.net\/<\/a><\/td>\n<\/tr>\n
DeepLNC<\/strong><\/td>\nPrediction of lncRNAs using deep neural network
\nhttps:\/\/bioserver.iiita.ac.in\/deeplnc\/index.php<\/a><\/td>\n<\/tr>\n
iSeeRNA<\/strong><\/td>\nPrediction of lncRNAs using support vector machine algorithm. CUHK (2014)http:\/\/137.189.133.71\/iSeeRNA\/<\/a><\/td>\n<\/tr>\n
RegRNA<\/strong><\/td>\nIdentification of regulatory RNA motifs
\nhttp:\/\/regrna2.mbc.nctu.edu.tw\/index.html<\/a><\/td>\n<\/tr>\n
spongeScan<\/strong><\/td>\nIdentification of miRNA spongeshttp:\/\/spongescan.rc.ufl.edu\/ <\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

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

List of key tools for identifying and annotating ncRNAs in plants miRPlant Identification of miRNAs…<\/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\/en\/wp-json\/wp\/v2\/pages\/168"}],"collection":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/comments?post=168"}],"version-history":[{"count":1,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/pages\/168\/revisions"}],"predecessor-version":[{"id":275,"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/pages\/168\/revisions\/275"}],"wp:attachment":[{"href":"https:\/\/sites.icgbio.ru\/plantgenomescollaboration\/en\/wp-json\/wp\/v2\/media?parent=168"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}