Practice(MCB104(Genomics(Problems((
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1.(What(are(contigs,(and(how(can(different(contigs(be(connected(together(in(a(
genome(assembly?(Answer(in(no(more(than(two(sentences.(
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2.(In(a(genome(assembly,(which((on(average)(are(longer((in(total(number(of(base(
pairs),(scaffolds(or(contigs?((Answer,(and(then(in(one(sentence(explain(your(answer.(((
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3.(In(what(linear(order(would(these(five(sequences(assemble(into(a(contig?(
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1. GCCGGAAAGCGCCGCTGTGGCTGAGA
2. ACTGGGTTGTTACATTCAAAAAAACT
3. TGGCTGAGAGCGAAGTTTCAGAGACTCTTA
4. GGAAGGCTACTGGCCGGAAAG
5. GAGACTCTTATTTAAACTGGGTTG
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All(sequences(are(on(the(same(strand.((Answer(just(with(the(linear(order(of(sequence(
reads(from(5’(to(3’.((Use(at(least(8(base(pairs(minimal(overlap(for(this(question.(
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4.((The(sequencing(of(tumor(genomes(is(often(done(to(look(for(chromosomal(
rearrangements(in(somatic(tumor(cells.((What(are(two(ways(that(paired(end(reads(
from(a(genomic(library(can(reveal(a(translocation?(((Hints:(the(first(way(uses(only(
single(sequencing(reads,(and(the(second(way(uses(information(from(both(sequencing(
reads(from(a(clone.(Both(ways(involve(aligning(the(tumor(genome(sequence(to(the(
normal(reference(human(genome(sequence.)!
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5.(If(you(used(Sanger(sequencing((with(two(sequencing(primers(complementary(to(
the(plasmid(vector(and(flanking(the(cloned(genomic(DNA(insert)(to(sequence(the(
paired(end(reads(of(one(4(kb(clone,(would(you(get(the(entire(4(kb(of(sequence(or(
would(you(have(a(gap(in(the(sequence(of(the(clone?((Answer(this(question(and(
explain(your(answer(in(no(more(than(one(sentence.((
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6.(What(does(EST(stand(for(and(how(would(you(generate(the(molecules(for(a(library(
to(collect(ESTs(from?(Your(answer(should(mention(two(different(types(of(nucleic(
acid(and(one(enzyme(covered(in(lecture.(((
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7.(How(can(aligning(EST(reads(to(genomic(DNA(sequence(reveal(the(positions(of(
introns?((
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8.((The(Philadelphia(translocation(is(a(chromosomal(abnormality(that(can(cause(
leukemia((blood(cancer)(and(involves(fusion(of(part(of(human(chromosome(9(to(
human(chromosome(22.((The(translocation(creates(a(fusion(gene,(in(which(part(of(
the(BCR(gene(is(fused(to(the(ABL(gene.((This(BCR_ABL(fusion(gene(speeds(up(cell(
division,(resulting(in(cancer.((Explain(in(no(more(than(four(steps,(each(not(longer(
than(a(sentence,(how,(starting(with(RNA(from(a(patient’s(blood,(you(could(try(to(
detect(this(or(any(other(fusion(genes(that(had(occurred(due(to(translocations(
between(different(chromosomes.(((
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