genome annotation with companion (part 2)...genome annotation with companion (part 2) you should...

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Genome Annotation with Companion (Part 2) You should have gotten an email indicating the status of your annotation (ie. job started and job complete). The email contains a link to the annotation output. • Explore your results with your group and discuss the annotation findings: o What does the genome statics tab tell you about your annotation? Are the results surprising? You can explore the reference genome you used in EuPathDB to help you assess the results. (For example, are you getting a reasonable number of genes? What about the GC content? Number of non-coding genes?)

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Page 1: Genome Annotation with Companion (Part 2)...Genome Annotation with Companion (Part 2) You should have gotten an email indicating the status of your annotation (ie. job started and

GenomeAnnotationwithCompanion(Part2)Youshouldhavegottenanemailindicatingthestatusofyourannotation(ie.jobstartedandjobcomplete).Theemailcontainsalinktotheannotationoutput.

• Exploreyourresultswithyourgroupanddiscusstheannotationfindings:

o Whatdoesthegenomestaticstabtellyouaboutyourannotation?Aretheresultssurprising?YoucanexplorethereferencegenomeyouusedinEuPathDBtohelpyouassesstheresults.(Forexample,areyougettingareasonablenumberofgenes?WhatabouttheGCcontent?Numberofnon-codinggenes?)

Page 2: Genome Annotation with Companion (Part 2)...Genome Annotation with Companion (Part 2) You should have gotten an email indicating the status of your annotation (ie. job started and

o Whatdoesthe“Resultfiles”tabcontain?WhatisanAGPfile?WhatisaGFF3file?

o Whatdoesthe“orthology”tabdisplay?Howmanypredictedproteins

fromyournewgenomeareincommonwithonesfromthereferencegenome?Howmanyareuniquetoyours?Whatdosingletonsrepresent(clickonthesingletonnumbertoseewhatthesegenesare?

Page 3: Genome Annotation with Companion (Part 2)...Genome Annotation with Companion (Part 2) You should have gotten an email indicating the status of your annotation (ie. job started and

o Whatdoesthephylogenytabrepresent?Doesitmakesense?

o ExaminetheSyntenytab–arethesegenomessyntenic?

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