GenomeAnnotationwithCompanion(Part1)Forthisexercisewewillstartwithanassembledgenomethatisunannotated.WewillobtaintheassembledFASTAfilesfromEuPathDBsites.CompanionishousedatSangerandcanbeaccessedhere:https://companion.sanger.ac.ukCompanion,isanonlinepipelinethatemploysdifferentsoftwaretoannotateandcompareanassembledsequencetoareference-annotatedgenome.ThefigurebelowillustratestheCompanionpipeline,thesoftwareusedandtheexpectedoutput.

Eachgroupwilldownloadoneofthegenomesasindicatedbelow.Group1–CryptosporidiumbaileyiTAMU-09Q1http://tinyurl.com/hgtddbzGroup2–CryptosporidiummeleagridisUKMEL1http://tinyurl.com/zskwvf5Group3–CryptosporidiumhominisUKH1http://tinyurl.com/zoxy48uGroup4–PlasmodiumcoatneyiHackerihttp://tinyurl.com/je4hftjGroup5–AcanthamoebapalestinensisReich(onlythelargest3000contigs)http://tinyurl.com/j2rd9lq

AllgenomesinEuPathDBsitesareavailablefordownloadformthe“DataFile”downloadsection,whichyoucanaccessfromtheDownloadsmenuinthegraytoolbar.

SelectingtheDataFilesoptiontakesyoutothedownloaddirectorieswhereyoucannavigatetothegenomeanddatatypeyouarelookingfor.

Todownloadspecificcontigs/scaffolds/chromosomesyoucanuseagenomicsequencesearchandplacethedesiredsequencesintoyourbasket.

a

-Onceyouhavedownloadedyoursequencefile,gototheCompanionsite:https://companion.sanger.ac.uk-Clickonthe“Annotateyoursequence”link.

-FollowtheinstructionsasdescribedontheCompanionwebsite:1.Providebasicinformationaboutthejobyouareabouttosubmit.Thisincludesajobname,speciesprefix(usuallythefirstletterofthegenusandthefirstthreelettersofthespecies:Acanthamoebapalestinensis=Apal).

2.Instep2,choosetheassemblyfilethatyoudownloaded.3.Instep3,indicateifyouwillbeusingRNAseqevidencetoguidetheannotation–inthisexercisewewillnotuseanyRNAseqdata.4.Instep4,selectthereferencesequenceyouwouldliketousetotransfertheannotationandtocompareyoursequenceto.Typicallyyouwouldliketouseareferencethatiscloselyrelated,soaphylogenetictreemightbeusefultolookat.HereareexamplesforPlasmodiumandCryptosporidium.ThereisonlyonereferenceforAcanthamoeba.http://tolweb.org/Plasmodium/68071http://tolweb.org/Cryptosporidium/124803

5.Instep5,thereafewmoreparametersyoumayonetoexamine.Forthepurposeofourexercisewewillkeeptheseatthedefaultvalues.

6.Enteryouremailaddresstogetanupdatewhenyourjobstartsrunningandwhenitiscomplete.Next,clickonthe“I’mnotarobot”captcha(CompletelyAutomatedPublicTuringtesttotellComputersandHumansApart).Finally,clickonthe“SubmitJob”link.