Bioinformatics Practical Test PDF

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Bioinformatics Practical Test The test is composed of twenty multiple choice questions. The information you require to identify the correct answers you will find online, however you must know some basics, for example: reading frames, typical eukaryote gene expression and gene structure, cytogenetic nomenclature, terms like homolog and conserved, inheritance patterns and pedigrees. The test is mostly based on the test DNA sequence shown below, which does not require editing. Internet links are indicated associated with a question. If no link is shown, the questions relate to the preceding link. You are required to work alone, but you can use your logbooks. You have 120 minutes to complete the test. You may not leave until the test is finished. Please record your answers on the answer sheet provided by filling in the appropriate circle using an HB pencil - as shown below. There is only one correct answer for each question. If two or more circles are filled in for any one question, it will be scored as incorrect even if it includes the correct response. If you want to change the answer use an eraser, or mark the wrong answer with an X. Q 1 2 3 4

a〇 a〇 a〇 a〇

b〇 b● b〇 b〇

c〇 c〇 c〇 c〇

d● d〇 d〇 d〇

e e e e

〇 ● 〇 〇

X

Test DNA Sequence >Test sequence

AAATAAAAGTGAAAGTTACCACGTCAGCCATATGCGGGTGTAAGAAGTCAGCCTCCATTCGGTTAGAGTA GACACAGGATTCCATGAGCTTTGATTACATCAGAGGGAATTATTGCCAGGTTTCCGTGACTTTGCTCAGT TACAAAAACATAATAGTCGAGGTTAAAAAAAATTTTTCTTTGTGATCTAAGCTTAAAACAATTGTTCGGT TTTTGCAAATAGTTTTTAGCAAATTACAGACACTATAAAATAAGACACTATATAATATTTCATTCCAAAA AGTGCAGTGATACTTTTCCAACTTTGTATAGTACAATCCAAGAGGATTTTTCTAAAATGTGAATTTTCAT TGATGTTTGTGAGAACCTCTAAAAAAGCTCTATTAAAAGGCAACATTTTATATGTGAATGTTGAGAGTGT AGGACAAACCTAGAAAAAAAAAAATGTGAGAGAGAGAGAGCGAAGAGCTGCAGATATAGAGAAAAGCACG TTTTCCGTGCATGCGCCTTTAATCTCATTCAATCACCCGCTCTTTGCCATCGAATCAGCTGTGAAATACA CTACCATGCAAAGCATTTATTATCTTCAATGGAAAAATATTTTTAAATTGGAAAAAACACCAGTGACATT GACCTGACACTGAAAACAAAATTATATAATACCGCATCATTAAACAACAGCATATGACTCAATGGCTCTA ATCGGTTAACTCAGAGTTCCACTTTAAATAACTTGACCTTTACAAATATTCTTTTTATTTTATGGAAATA ATAATTAGGTCAGTTCAGTAAAATAATCCAACACTTGATTGATAGCTATCTCTGTAGCCGTTGTTATCTT TTTCAGTAGGAACATATGTAACTTTGAGTTACTTGATTTTGGTTGTCAGACTGTGCGGATCGTATACGAA ATTTTAGTCCAAATTTTTAGTTTTATTTTTTACCTCGAAATATTTCAAAATTCTGTGCTTACGCAATGGT TTCCAATCATCCGCGCCGCTGCGAATTCGATAGCTAGCTTATTAAAACACAATGTCCGCTACTCTTTTTC ATCCAACAAAATAACACCACACCAAATCAAACGTAAATGGATCTTCGTGCTGCAGAACTACACTCGAATC TCAAAAATGACGACCTACTTCAACTACCCCAGCAAGGAGCTGCAGGATGAGCTGCGCGAAATCGCCCAGA AAATCGTTGCCCCCGGCAAGGGAATCCTCGCCGCCGATGAGTCCGGCCCAACCATGGGCAAGCGTCTGCA GGACATCGGCGTGGAGAACACCGAGGACAACCGCCGTGCCTACCGTCAGCTGTTGTTCAGCACTGACCCC AAGCTGGCCGAGAACATCTCTGGAGTGATCCTGTTCCACGAGACCCTCTACCAGAAGGCCGATGATGGCA CCCCCTTCGCCGAGATCCTGAAGAAGAAGGGAATCATTCTGGGCATCAAGGTCGACAAGGGTGTTGTCCC ACTGTTCGGCTCTGAGGATGAGGTCACCACCCAGGGTCTGGATGACCTGGCCGCCCGTTGCGCCCAGTAC AAGAAGGACGGTTGCGACTTCGCCAAGTGGCGTTGCGTCCTGAAGATCGGCAAGAACACCCCATCCTACC AGTCGATCCTGGAGAACGCCAATGTCCTGGCCCGCTACGCCTCCATCTGCCAGTCGCAGCGCATCGTCCC AATTGTGGAGCCCGAGGTTCTGCCCGATGGCGATCACGATCTGGACCGCGCCCAGAAGGTCACCGAGACC GTCCTGGCCGCCGTCTACAAGGCCCTGAGCGACCACCACGTCTACCTGGAGGGTACTCTGCTGAAGCCCA ACATGGTCACCGCCGGTCAGTCGGCCAAGAAGAACACCCCCGAGGAGATCGCCCTGGCCACCGTGCAGGC TCTGCGCCGCACCGTTCCCGCCGCCGTTACTGGTGAGTCATCAAATCCAACTGTAATCTCTGGATTGGAA TGCATTCACCTTGTTTTTGCAATGAATCCTATCTAATCGATTGTTTGTCTACAGGCGTGACCTTCCTGTC TGGAGGTCAGTCCGAGGAGGAGGCCACCGTCAACCTGAGTGCCATCAACAACGTTCCCTTGATCCGCCCA TGGGCCCTCACCTTCTCGTACGGTCGTGCCCTGCAGGCCTCCGTCCTGCGTGCCTGGGCTGGCAAGAAGG AGAACATCGCTGCCGGCCAGAACGAGCTGCTTAAGCGCGCCAAGGTGAGTCCTTGGATAGTTGTATCTAT GCACGATTGATTGCAGTTAGCAATTTAAGTGGTGAATGTATTAAGAGTGTCAGGTATATGCTTCGGAAGT ATTCCTTGGGCTAAGAAATATTATACATGTATAATATAACATACAGCATATTCCCAGCCATTGATTCCAT TTCCAATCCCAAATGACCACAATGTTCTTCTAATCCTCTAATCTTATCCCTTTTATTTCCCTACCATTAT TTGTAACCTTTTTTTGCTTTTGTACGTGAGACATTAATTTCATCATCAATAACCACACATTAATCATGCC TAGGCTAACGGAGAGGCGGCTTGTGGTAACTATACAGCTGGATCGGTTAAGGGGTTCGCTGGAAAAGATA CTTTGCATGTGGATGACCACAGGTATTGATCAAAGGATTGAAGAATTGCTGCCTTAAGATGGCGATGAAC AAGCTTTCATGGGGTAACTTAAGAATCATAGCCGCCTTTCACCAAATCCGACTTATCGCAAACGCCTTTA ACATACTGTCCTCGTGCCACTCATGCTTCGCTTGCTCTAAACCTAATCCACAAAAGCCCAAAATCTGATT AATCCCAACCAAAATCCCGCTCTCCTCCCGCTTCCACAGGCCAATTCCCAGGCCTGTCAGGGTATTTACG TGCCCGGCTCAATTCCGTCGTTTGCCGGCAATGCCAACCTCTTTGTCGCCCAGCACAAATACTAAGTCCT AAATGCCACGCACTAATCCCGAGTCACAATCGAGCGAAGCTATATCCCAAGCCGAATCCAGATAATCCGC AAGAGTTACTGATCGAGGCCCAGCTGGAGTGAGACGGGCAACATTTATATTCCTCCAACAATGGAACTGC AAATATATTCCTTTTATACATTTTTACATTTTACCGAATAAACTGACTAGACCTTAAAGAAAATATTTTT

Questions

1. From the inferred translation of the test DNA sequence, what are the first five amino acid residues in the longest peptide predicted (starting from a methionine)? a. b. c. d. e.

IKVKV MTTYF KNIFF MSATL MLPVS

ExPASy - Translate tool http://web.expasy.org/translate/ (hint: don’t include the sequence heading) 2. From the inferred translation of the test DNA sequence, which reading frame contains the longest open reading frame? a. b. c. d. e.

5’3’ 5’3’ 5’3’ 3’5’ 3’5’

Frame 1 Frame 2 Frame 3 Frame 1 Frame 2

ExPASy - Translate tool http://web.expasy.org/translate/ 3. The test DNA sequence contains a gene or at least part of a gene, based on a predicted gene structure how many exons might it have? a. b. c. d. e.

None Three Four Five Six

Genescan http://genes.mit.edu/GENSCAN.html 4. Based on a predicted gene structure, what is the length of the longest intron? a. b. c. d. e.

121 626 182 796 825

5. How long is the predicted peptide coded by the test DNA sequence based on the predicted gene structure? a. b. c. d. e.

200 aa 796 aa 363 aa 96 aa 6 aa

6. For a long DNA sequence, Genescan is often more useful than ExPASy for predicting a protein sequence because it: a.

takes into account open reading frames and consensus sequences to predict exon boundaries

b. c. d. e.

ignores start and stop codons is just a better programme predicts genes based on consensus sequences not open reading frames converts the sequence to cDNA

7. What is the gene most likely to code for and in what organism? a. b. c. d. e.

AGAP002564-PA, Anopheles gambiae Aldolase, Drosophila melanogaster YQE_11479, Dendroctonus ponderosae Hypothetical protein DAPPUDRAFT_188180, Daphnia pulex putative fructose 1,6-bisphosphate , Homalodisca vitripennis

Genescan http://genes.mit.edu/GENSCAN.html BLASTP search http://blast.st-va.ncbi.nlm.nih.gov/Blast.cgi

8. What is the most closely related homologue of this gene called in humans? a. b. c. d. e.

Aldolase B Thrombospondin type-1 containing protein Aldolase C KIAA1679 protein Aldolase A

BLASTP search http://blast.st-va.ncbi.nlm.nih.gov/Blast.cgi (hint: edit and resubmit)

9. How many exons does transcript 009 of the human homolog have? How many transcripts does the gene have in total? a. b. c. d. e.

20 exons and 22 transcripts 14 exons and 23 transcripts 27 exons and 14 transcripts 14 exons and 27 transcripts 10 exons and 29 transcripts

Ensemble http://www.ensembl.org/index.html (hint: link from genpept; gene tab in ENSEMBL)

10. On what chromosome is the most closely related human homolog located? a. b. c. d. e.

16 X 9 7 20

Ensemble http://www.ensembl.org/index.html (hint: same page) 11. How many different homologs does this gene have in humans? a. b.

Eight, A to H Two, A and B

c. d. e.

Three, A, B and C Four, A, B, C and D Two, X and Y

Online Mendelian Inheritance in Man (OMIN) http://omim.org/ (hint: search with the gene name; gene tab)

12. Which of the human homologs is/are expressed in the developing embryo? a. A b. A and B c. C d. H e. X and Y

13. Which of the human homologs is expressed and which one is repressed in adult liver, kidney, and intestine? a. b. c. d. e.

A expressed, B repressed C expressed, B repressed H expressed, Y repressed X expressed, D repressed B expressed, A repressed

14. What genetic disorder is associated with gene homolog A? a. Diabetes b. Fructose intolerance c. Glycogen storage disease XII d. Alcoholism e. Sugar allergy

15. What is the chromosome position for homolog B? a. b. c. d. e.

9q31.1 16p11.2 17q11.2 10q27.2 Xp12.1

16. What is the evolutionary relationship between the homologs in vertebrates? a. b. c. d. e.

They share a common ancestor and are paralogous, with B diverging first They derive from different ancestors, therefore paralogous, with A diverging first They share a common ancestor and are orthologous, with A diverging first They are new genes and therefore orthologous, with B emerging first They derive from different ancestors and therefore orthologous, with X diverging first

17. What is the genetic disorder associated with the human homolog B? a. Diabetes b. Fructose intolerance c. Glycogen storage disease XII

d. Alcoholism e. Sugar allergy Online Mendelian Inheritance in Man (OMIN) http://omim.org/ (hint: search with name for homolog B)

18. What is the inheritance pattern of the genetic disorder associated with the human homolog B? a. b. c. d. e.

Autosomal dominant Sex-linked recessive Autosomal recessive Sex-linked dominant Autosomal co-dominant

19. If both parents are known to be heterozygous for the homolog B associated disorder, what is the probability that they will have a child with the disorder? a. b. c. d. e.

100% 75% 65% 50% 25%

20. There is another non-functioning homolog on chromosome 10q, which is referred to as: a. b. c. d. e.

an isomer a pseudogene a spare copy a microRNA a transposon...