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Example questions for Bioinformatics, Study notes of Bioinformatics

Applied Science University (ASU)Bioinformatics

It is a sample of possibilities. Example questions. 1. You are given two DNA sequences to align. ACGTCCTTCATT and GTCTCATG. You have a scoring scheme where a.

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Example questions for Bioinformatics, first semester half

Sommersemester 2011

Note

• Die schriftliche Klausur wird in deutsch geschrieben.

• The questions will be based on material from the Übungen and the Lectures.

• These are typical questions. It is not a "Fragenkatalog". It is a sample of possibilities.

Example questions

You are given two DNA sequences to align

ACGTCCTTCATT and GTCTCATG

You have a scoring scheme where a

• match gives you +1

• a mismatch gives you 0

• gap opening costs −10

Write down the best alignment of the two sequences

You have a scoring scheme where

• A match gives you +1

• a mismatch gives you −1

• opening a gap costs you −1

Write down the best alignment for the same two DNA sequences.

Discover Study notes of Bioinformatics Applied Science University (ASU)

Partial preview of the text

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Example questions for Bioinformatics, first semester half Sommersemester 2011 Note • Die schriftliche Klausur wird in deutsch geschrieben.

Example questions^ •^ •^ The questions will be based on material from the Übungen and the Lectures.These are typical questions. It is not a "Fragenkatalog". It is a sample of possibilities.

1. You are given two DNA sequences to align ACGTCCTTCATT and GTCTCATG You have a scoring scheme where a • match gives you +

2. Write down the best alignment of the two sequencesYou have a scoring scheme where^ •^ •^ a mismatch gives you 0gap opening costs^ −

Write down the best alignment for the same two DNA sequences.^ •^ •^ •^ A match gives you +1a mismatch gives youopening a gap costs you^ −1^ −

3. You are aligning protein sequences using a substitution matrix : A R N D -1-2-2 A 4 -1-2R 50 -2N 061 -2-2D 16 -3-3-3C 0 -1Q 100 -1E 002 -2-1G 00 -2-1H 01 -1-3-3-3I -1-2-3-4L -1-1K 20 -1-1-2-3M -2-3-3-3F -1-2-2-1P -1S 110 -1-1T 00 -3-3-4-4W -2-2-2-3Y -3-3-3V 0

C Q E G H I -1-1-2-1 00 -3-2-3 100 -3-3 0001 -3-1-1-3 02 -3-4-3-3-1 9 -3-2-3 520 -4-2-3 250 -3-2-2-2-4 6 -3-2-3 008 -1-3-3-4-3 4 -1-2-3-4-3 2 -3-2-1-3 11 -1-2-3-2 01 -2-3-3-3-1 0 -3-1-1-2-2-3 -1-1-2 000 -1-1-1-2-2-1 -2-2-3-2-2-3 -2-1-2-3-1 2 -1-2-2-3-3 3

L K M F P S -1-1-1-2-1 1 -2-1-3-2-1 2 -3-2-3-2 01 -4-1-3-3-1 0 -1-3-1-2-3-1 -2-3-1 100 -3-2-3-1 10 -4-2-3-3-2 0 -3-1-2-1-2-1 -3-3-2 210 -2-3-2 420 -2-1-3-1 50 -1-2-1 250 -3-4-2 006 -3-1-2-4-1 7 -2-1-2-1 04 -1-1-1-2-1 1 -2-3-1-4-3 1 -1-2-1-3-2 3 -2-1-2-2 11

T W Y V Gap opening costs -8. Gap widening (extension) costs -1. -3-2 00 -1-3-2-3 -4-2-3 0 -1-4-3-3 -1-2-2-1 -1-2-1-2 -1-3-2-2 -2-2-3-3 -2-2-3 2 -1-3-1 3 -1-2-1 1 -1-3-2-2 -1-1-1 1 -2-1 13 -1-4-3-2 -3-2-2 1 -2-2 50 -2 11 -3 2 -2-1 27 -3-1 04

You are given an alignment AACDQRST A-CD-RST What is the score of this alignment?

4. Given AACDQRST A-CD--ST What is the score of this alignment?

5. 6. A A-CD-SST What is the score of this alignment ?You have calculated a score matrix for a pair of DNA sequences. You have performed the tracebackACDQRST

calculation and found a result like:

7. Write down the corresponding sequence alignment with gaps in the correct positions.Outline the steps used to find values for a BLOSUM amino acid similarity matrix.

C C A^ A^ C^ A^ C^ C^ T^ T^ A

T C C A

A

26. From a multiple sequence alignment, I have calculated variability/conservation as a function of sequence

27. position:conserved. Why might they be important residues ?In the picture above, some sites are not very conserved. I say these residues cannot be important to thefunction of the protein. Why may I be wrong?^ Residues 37 and 43 seem to be very

28. 29. I have calculated a sequence alignment of 400 tyrosine kinases and I find that very few sites seem to beconserved in evolution. How could I change my results, so that more sites seem to be conserved ?We have a family of sequences and all pair-wise alignments. I can count the number of differences(mutations) between any two sequences and calculate the fraction of residues that have changed :

30. This is not a good measure. Why not ?I want to use aligned DNA sequences to build a phylogenetic tree. Name two reasons that the branches inthe tree may not be reliable. p^ mut^ =^ Ndiff N^ length. I would like to estimate evolutionary time by saying^ t^ =^ k^ p^ mut^ for some constant^ k.

31. 32. I have built a phylogenetic tree using a neighbour joining method. Describe a general approach I could useto see how reliable the tree is.It is believed that protein sequence evolves and changes faster than protein structure. What could be anevolutionary explanation for this.

33. 34. Which graphical representation would you use in order to emphasize the secondary structure content ofprotein? all-atom, chaintrace, ribbon, ...?You have a protein of unknown function from a bacterium. You have made a knock-out mutant, but thebacteria die immediately without the corresponding gene. You have sequenced the protein. What steps

35. would you take to guess the function of the protein? What kind of information would you look for ?Wie würden Sie vorgehen um in einem Multiplen Sequenzalignment potentiell katalytisch wichtigeSeitenketten im aktiven Zentrum zu identifizieren?

0 50 residue number 100