ncbi本地blast 安装方法

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1、INHOUSELOCALBLASTSEARCHTogetstartedyouneedtheblastall.exeandformatdb.exe(FromNCBI).Therestoftheperlandbatchprogramsyoumightneedtochangethepathofthedirectoriestheyarepointingtoortheblastoptiontheyuse,couldbedownloadedfrom:http://psi081.ba.ars.usda.gov/SGMD/software/blast/Blast.htmFo

2、rtheprogramstoworkwithoutmodifyingthepaths,thewholefolder“Blast.zip”shouldbeunzippedtoafolder"Blast"movedunderthe“C:”directory.Forquestionsorcommentspleasecontact:ImedBenChouikhabchouikh@gmu.eduI.Stepone:Blasting1)Downloadthedatabasethatyouwanttoblastagainst,forexampletheNTdatabase

3、fromNCBI.Ifyouwanttousealocaldatabase,storeallthesequencesinatextfile.ThefileprovidedbyNCBIisazipped(nt.gz)filesoyouhavetounzipit.2)AttheDOSprompt(whichyoucangettofromwindowsbychoosing:Start,Run,thentyping:command),runformatdb.exetocreatealocaldatabasefromthattextfileorthedownloade

4、ddatabase.Usage:formatdb–tdatabasename–iinputfile–pFExamples:1)formatdb–tnt–int–pF2)formatdb–tsnc–iinputfile–pFdatabasenameisthenameyouwanttogivetoyourdatabaseinputfileisthenameofthetextfilethatcontainsyoursequencesorthenameofthedatabasethatyoudownloadedfromGenBank(technicallyalsoa

5、textfileofsequences).Moreaboutformatdb.exeinformationandcommandoptionscanbefoundhere:http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/formatdb.txt3)OpenthefileBlastList.pl(usingNotepadoryourfavoritetexteditor)Makethesmallchangesasinstructedinthefilethensaveit.Theseareth

6、eonlytwochangesthatshouldbemadetoruntheprogram.4)RunBlastList.plasfollows:c:>cdBlastc:>BlastperlBlastList.plThefileBlastList.plautomaticallycreatesabatchfile“DosBlast.bat”dependingonthelistofthesequencetobeblasted.5)RunDosBlast.batc:>BlastDosBlast.batDosBlast.batistheactualfile

7、thatdoestheblastsearch.II.Steptwo:Extractingdatafromblastresults6)Movealltheresulting".txt"filestoBlastOut7)GotothedirectoryBlastOutc:>BlastcdBlastOut8)RunHits.plc:>BlastBlastOutperlHits.plThatwillmovethefilesthatreturnednohitstoadifferentdirectory9)RunDataExt.plc:>BlastBlas

8、tOutperlDataExt.plTheoutp