SNPHunter User Manual 17x.docx
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SNPHunter User Manual 17x.docx
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SNPHunterUserManual17x
SNPHunter1.7xUserManual
Introduction
Thisprogram,SNPHunter,wasdevelopedforSNPsearchingandmanagementunderthejointguidanceofTianhuaNiu,SiminLiuandXinXuwithintheHarvardSchoolofPublicHealth.ItwaswrittenbyLinWang,adoctoralcandidateinHSPH.TheprimaryobjectiveistofacilitategeneticstudywithSNPsearchingandmanagement,includingfetchingSNPflankingsequenceanddetectingnearbySNPsandfilteringSNPs.LocalizedSNPdatasetanduserfriendlyinterfacegivesresearcheraneasyandfastwaytosearchandorganizeSNPs,greatlyfacilitategeneticstudies.
Installation
Windowsoperatingsystem(includingWin98,Win2000,NTandWinXP)with.NETFrameworkinstalled.NETFrameworkcouldbefreelydownloadedfromMicrosoftwindowsupdate.WindowsXPisrecommendedandyoumusthaveyoursystemupdatedwithnecessaryservicepackifyouarenotrunningWindowsXP.
Thereisnoothercomponentthatneedstobeinstalledexcepttheexecutablefile“SNPHunter.exe”.
SNPSearch
Usershoulddefinegenesymbolin“Genesymbol”box,forexample,“TNF”whichislocuslinknamefor“tumornecrosisfactor”withlocusID7124.Usercanchooseidealfunctionclassingeneregionand/orup-stream/down-streamregionassearchcriteria.Oncebothofthemarechecked,SNPHunterwillsearchbothregions;otherwise,onlycheckedregionwillbesearched.Withheterozygositycriteria,usercanrestrictSNPsfoundtobeabovecertainheterozygosityvalue.Afterclickingon“SNPSearch”button,allSNPsthemeetusersearchcriteriawillbelistedinthesnplistbox.
DirectSNPSearch
DirectSNPSearchoffersuseraversatilemethodtosearchSNPfromdbSNP.UsercansearchalltheSNPrelatedwithadiseasethathe/sheinterestsin,like“cysticfibrosis”;orjustsearchforaspecificSNPlike“rs12345”.Afterclickingon“DirectSNPSearch”button,allSNPsthemeetusersearchcriteriawillbelistedinthesnplistbox.ItmaytakealongtimeforthesystemtoreturnalltheSNPsthatmeetyourcriteriaifyouaresearchingapopularcomplexdisease,likehypertension.Actually,“DirectSNPSearch”cantakeanyquerythatisacceptableindbSNPEntrez,thatmeansusercanevenusesomecomplicatequerieswithunionorjoin.
FetchSNPInfo
AfterSNPsearch,usermightwanttoknowdetailsofeachSNPthatlistedintheSNPlistpanel.“FetchSNPInfo”willretrieveSNPsummaryindbSNPforeachlistedSNP.Afterclickingonthe“FetchSNPInfo”button,aprogressbarwillappeartoshowtheretrievalprogressandwilldisappearonceretrievalisdone.Afteritfinishes,thecorrespondingSNPsummarywillbeshownatSNPinfopanelwhenuserclickoneachSNPitem.
SelectSNP
ClickingontheSNPiteminSNPlistpanelwillselectorde-selectthatSNPitem.ThenumberoftotalandselectedSNPswillbeshown.OnceSNPinfoisfetched,usercanviewthesummaryofeachSNPandmakeaselectiondecisionuponthat.Allofthefunctionslike“SaveSNPSet”,“SaveFlankingSeq”onlydealwithselectedSNPs.
SaveSNPSet
UsercansavetheSNPlist(includingSNPinfoifretrieved)thatreturnedfromdbSNPtoalocalfilesothatusercanviewthemlaterwithoutretrievingthemagain.Clickingon“SaveSNPSet”button,a“SaveAs”windowwillpopupaskinguserforthefiletosaveSNPset.SNPsetlistwillbesavedwithextension“.sls”whichstandsfor“SNPlist”,SNPinfowillbeAUTOMATICALLYsavedwithextension“.sif”whichstandsfor“SNPinfo”andsharethesamenameastheSNPlistfile.Forexample,ifusersavestheSNPlistto“IL2.sls”,thentheSNPs’info(ifretrieved)willbesavedas“IL2.sif”inthesamedirectory.
LoadSNPSet
UsercanloadtheSNPlist(includingSNPinfoifsaved)thatsavedinalocalSNPlistfile(.sls)sothatusercanviewthemlaterwithoutretrievingthemagain.Clickingon“LoadSNPSet”button,a“OpenFile”windowwillpopupaskinguserforthelistfilewhereSNPsetisstored.SNPsetlistshallbesavedwithextension“.sls”whichstandsfor“SNPlist”,SNPinfowillbeAUTOMATICALLYloadedwithextension“.sif”whichstandsfor“SNPinfo”andsharethesamenameastheSNPlistfile.Forexample,ifuserloadstheSNPlistof“IL2.sls”andthereisa“IL2.sif”inthesamedirectory,thentheSNPs’infowillalsobeloadedintoSNPHunter.ThecorrespondingSNPinfosummarywillbeshownatSNPinfopanelwhenuserclicksoneachSNPitem.IfthereisnotSNPinfosummaryshown,usershouldretrieveSNPinfofirst.Pleasereferto“FetchSNPInfo”sectionfordetails.
UsercanalsoeditaSNPlistfileusinganyTextEditor.TheformatisoneRSnumberperline,like“rs12345”.Inthisway,usercandealwithSNPsetthatisnotobtainedfrom“SNPSearch”Function.
SaveFlankingSeq
UsercanretrieveSNP’sflankingsequenceofanylengthafterSNPinfohasbeenretrieved.WithSNPlocationinformationineachSNPinfo,SNPHunterwillgotoNCBItodownloadthesequenceofthelengththatuserspecifies.Besides,SNPHunterwillalsodetectanyreportedSNPwithinthatregionandmodifiesthesequencewiththoseSNPs’alleleinformation.Forexample,theremightbea“S”inthesequencewhichmeansthereisaSNPatthispositionwhoseallelesare“C”and“G”.
Clickingonthe“SaveFlankingSeq”button,a“SaveAs”windowwillpopupaskingforthelocationofthefilewheresequencesaretobesaved.Theextensionofthefileshouldbe“.seq”.Usercanalsospecifythelengthoftheflankingsequence.Forexample,“250bp”meansuserwants250upstreamand250downstreamflankingsequence.
DetectNearbySNP
“DetectNearbySNP”functionoffersuserawaytodetectexistenceofnearbySNPs.Like“SaveFlankingSeq”,thisfunctionworksonlyafterSNPinfohasbeenretrieved.WithSNPlocationinformationineachSNPinfo,SNPHunterwillgotodbSNPtosearchforanySNPthatliewithinthisregion.
Clickingonthe“DetectNearbySNP”button,a“SaveAs”windowwillpopupaskingforthelocationofthefilewherethedetectresultsaretobesaved.Theextensionofthefileshouldbe“.snp”,whichwillcontainthesnp’slocation(contigandposition)andnearbySNPrsnumbers.Usercanalsospecifythelengthofthedetectingregion.Forexample,“250bp”meansuserwantstosearch250upstreamand250downstream.
CreateSNPSummarybyLocuslink
“CreateSummarybylocuslink”functionoffersuserapowerfulwaytocollectalltheSNPsbelongingtocertaingene.Usershouldusetexteditortoeditagenelistfilewithextension“.gls”whichstandsfor“genelist”.TheformatofthatfileisoneLocusLinkIDNumberperline.Like“3558“whichistheIDforgene“Interleukin2”.
Clickingonthe“CreateSummary”button,a“SaveAs”windowwillpopupaskingforthelocationofthefilewherethesummaryresultsaretobesaved.Theextensionofthefileshouldbe“.summary.txt”,whichwillcontainalltheimportantsnpinformationlikeHeterozygosity,function,locationetc.Theresultfileistab-delimitedtextfilethatcanbeopenedbyanytexteditororExcel.Andthisfilewillbetheinputfor“SNPFilter”function.
FilterSNP
Usercanuse“FilterSNP”functiontoselectSNPsinteractively.SNPHunterwillusethesummaryinformationsavedfrom“CreateSummary”togiveauserfriendlyinterfaceandautomaticSNPselection.
Clickingonthe“FilterSNP”button,“SNPFilter”windowwillcomeup.Usershouldloadsummaryfilefirstbyclickonthe“Load”button.Then,a“OpenFile”windowwillpopupaskingforthelocationofthefilewherethesummaryresultsweresaved.Theextensionofthefileshouldbe“.summary.txt”.OncethesummaryfileisloadedinSNPHunter,“SNPFilter”windowwilldisplaylikethefollowingpicture.
SNPPanel
ItdisplaystheSNP’sinformationasfollowing:
“Pick”showswhetheruserpicksthisSNPornot.Ifitis“1”,itmeans“selected”;“0”meansnot.Filterfunctionwillchangethisvalue,andusercanmodifyitatanytime.
“Gap”showsthedistancebetweenthisSelectedSNPandtheclosestSelectedSNP.
“Nearby”showsthedistancebetweenthisSNPandtheclosestSNP.
“Position”showsthepositionoftheSNPinthecontig.(contiginformationisomitted)
“RS”showsthersnumberofthatSNPindbSNP.
“Het”showstheheterozygosityoftheSNP.
“Function”showsthefunctionclassoftheSNP.
“Validation”showsthevalidationinformationoftheSNP.LikeindbSNP,“2”meanswith2hit,“C”meansbycluster,“F”meansbyfrequency,“H”meanswithHapMapfrequencyand“S”meansbysubmitter.
“LocusLink”showsthelocuslinkIDoftheSNP.
FilePanel
“Load”willloadSNPsummaryfileintoSNPHunter.
“SaveAs”willsaveanewSNPsummaryfilewithonly“Pick”equal“1”.
GeneListPanel
AlltheloadedlocuslinkIDwillshowsinthispanel.
“ALL”representallthegenes.
ClickoneachlocusIDitemwillonlydisplaytheSNPofthatgene;andfilterfunctionalsoonlyappliestothatgene.
RefreshPanel
When“PickedOnly”ischecked,onlythoseSNPwith“Pick”valueequal“1”willbedisplayed.ThisgivesusersaclearpictureofthoseselectedSNPs.
Clickon“Refresh”buttonrefreshtheSNPdisplayinSNPpanel.Itisusefulwhenusermanuallychangesthe“Pick”valueandwantstohavealookoftheresult.
FilterPanel
FilterpaneloffersuserawaytoautomaticallyfilterSNPsaccordingtothecertaincriteria.Ofcourse,usercanmanuallyselect/de-selectSNPatanytimebymodify“Pick”valuebetween“1”and“0”.
“Mustkeep”isthewaytokeeptheimportantSNPs,likecodingsynonymous/non-synonymousSNP.Oncechecked,thoseSNPswillalwaysstayregardlessofotherfilteringcriteria.
“Optional”givesuseranoptiontokeepenoughSNPsforgeneticstudyeventheSNPlooksnotth
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