miRNA靶基因预测.pdf

miRNA靶基因预测有⼈问miRNA靶基因如何预测的问题，鉴于⾃⼰也做过相关的分析，稍有点经验，总结记录⼀下。⼀、miranda预测1.软件安装$wgethttp://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz$tar-xvfmiRanda-aug2010.tar.gz$cdmiRanda-3.3a/$./configure--prefix=/Lustre01/user/software/miRanda-3.3a/$make&&makeinstall$cd***/miRanda-3.3a/bin#你⾃⼰的软件路径$./miranda--help#产看帮助信息和参数等等，具体如下=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=mirandav3.3amicroRNATargetScanningAlgorithm=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=(c)2003MemorialSloan-KetteringCancerCenter,NewYorkAuthors:AntonEnright,BinoJohn,ChrisSanderandDeboraMarks(mirnatargets(at)cbio.mskcc.org-reachesallauthors)Softwarewrittenby:AntonEnrightDistributedforanyonetouseundertheGNUPublicLicense(GPL),Seethefiles'COPYING'and'LICENSE'fordetailsIfyouusethissoftwarepleasecite:EnrightAJ,JohnB,GaulU,TuschlT,SanderCandMarksDS;(2003)GenomeBiology;5(1):R1.mirandacomeswithABSOLUTELYNOWARRANTY;Thisisfreesoftware,andyouarewelcometoredistributeitundercertainconditions;type`miranda--license'fordetails.miRandaisanmiRNAtargetscannerwhichaimstopredictmRNAtargetsformicroRNAsusingdynamic-programmingalignmentandthermodynamics.Usage:mirandafile1file2[options..]Where:'file1'isaFASTAfilewithamicroRNAquery'file2'isaFASTAfilecontainingthesequence(s)tobescanned.OPTIONS--help-hDisplaythismessage--version-vDisplayversioninformation--licenseDisplaylicenseinformationCorealgorithmparameters:-scSSetscorethresholdtoS[DEFAULT:140.0]-en-ESetenergythresholdto-Ekcal/mol[DEFAULT:1.0]-scaleZSetscalingparametertoZ[DEFAULT:4.0]-strictDemandstrict5'seedpairing[DEFAULT:off]Alignmentparameters:-go-XSetgap-openpenaltyto-X[DEFAULT:-4.0]-ge-YSetgap-extendpenaltyto-Y[DEFAULT:-9.0]GeneralOptions:-outfileOutputresultstofile[DEFAULT:off]-quietOutputfewereventnotifications[DEFAULT:off]-trimTTrimreferencesequencestoTnt[DEFAULT:off]-noenergyDonotperformthermodynamics[DEFAULT:off]-restrictfileRestrictsscanstothosebetweenspecificmiRNAsandUTRsprovidedinapairwisetab-separatedfile[DEFAULT:off]OtherOptio