Bioinformatics Interview Questions and Answers

What is bioinformatics?

Bioinformatics involves the integration of computers, software tools, and databases in an effort to address biological questions. Bioinformatics approaches are often used for major initiatives that generate large data sets. Two important large-scale activities that use bioinformatics are genomics and proteomics. Genomics refers to the analysis of genomes. A genome can be thought of as the complete set of DNA sequences that codes for the hereditary material that is passed on from generation to generation. These DNA sequences include all of the genes (the functional and physical unit of heredity passed from parent to offspring) and transcripts (the RNA copies that are the initial step in decoding the genetic information) included within the genome. Thus, genomics refers to the sequencing and analysis of all of these genomic entities, including genes and transcripts, in an organism. Proteomics, on the other hand, refers to the analysis of the complete set of proteins or proteome. In addition to genomics and proteomics, there are many more areas of biology where bioinformatics is being applied (i.e., metabolomics, transcriptomics). Each of these important areas in bioinformatics aims to understand complex biological systems.
Many scientists today refer to the next wave in bioinformatics as systems biology, an approach to tackle new and complex biological questions. Systems biology involves the integration of genomics, proteomics, and bioinformatics information to create a whole system view of a biological entity.

What is Computational Biology?

Computational biology is an interdisciplinary field that applies the techniques of computer science and applied mathematics to problems inspired by biology. Major fields that use computational biology techniques include:

* Bioinformatics, which applies algorithms and statistical techniques to biological datasets that typically consist of large numbers of DNA, RNA, or protein sequences. Examples of specific techniques include sequence alignment, which is used for both sequence database searching and for comparison of homologous sequences; gene finding; and prediction of gene expression. (The term computational biology is sometimes used as a synonym for bioinformatics.)

* Genomics, which studies the genomes of cells and organisms by high-throughput genome sequencing that requires extensive post-processing known as genome assembly, and which uses DNA microarray technologies to perform statistical analyses on the genes expressed in individual cell types.

* Systems biology, which aims to model large-scale biological interaction networks (also known as the interactome), often using differential equations.

* Protein structure prediction and structural genomics, which attempt to systematically produce accurate structural models for three-dimensional protein structures that have not been solved experimentally.

* Computational biochemistry and biophysics, which make extensive use of structural modeling and simulation methods such as molecular dynamics and Monte Carlo-inspired Boltzmann sampling methods in an attempt to elucidate the kinetics and thermodynamics of protein functions.

Sample Interview Questions: Bioinformatics

1. Tell me about the different kinds of DNA sequences.

There are three kinds of DNA sequences. Genomic DNA comes from the genome and includes both genes and extragenic material. cDNA is reverse transcribed from mRNA and corresponds only to the expressed parts of the genome. Recombinant DNA is man-made and is composed of artificial DNA.

2. If you had 1,500 base pair pieces of random DNA and you wanted to know how many of them had homology to known genes, what would you do to determine that?

I would use a BLASTX search against a known protein database - such MCBI's NR database. I would then sort them to determine how many were unique.

Sample Interview Questions: Discovery Research in Biotech

1. What technique is used to measure the number of copies of a gene or an RNA molecule in human tissues?

PCR or polymerase chain reaction in real time, as opposed to the conventional method, because the number of copies of the target molecule can be monitored for each PCR cycle.

2. What are the limitations of blotting techniques and what alternatives can you suggest?

The major limitation of blotting procedures is the length of time needed and the fact that they can accommodate only one probe at a time. DNA microchip technology permits the analysis of thousands of genes at the same time. DNA molecules are attached to the wafers in an organized array and are called the probes. DNA molecules taken from tissues are hybridized to the chips and are called targets, which are labeled with fluorescent light. The probes that have hybridized to the fluorescent targets are then identified by fluorescence microscopy.

1. Can you give me an example of a project you were involved with that illustrates your interest and skills in bringing people together?

I was the founder of the biotechnology club at my college. Although several other people co-founded the group, it was created at my initiative. We set up seminars where I got several key people in the industry to come speak to us on hot topics in the industry - like the agricultural biotech controversy and the ethical dimensions of stem cell research. The biotech club also sponsored a career fair, where we got over 100 students, soon to graduate, connected with over a dozen companies. I personally approached about half of those companies. I feel really proud about my contribution to this project.

2. How would you value a biotech company as opposed to a consumer products company?

Most companies are valued based on their growth prospects. That's what determines their stock price and overall dollar value, when they are sold. Biotech companies, as are other pharmaceutical companies, are valued based on the perceived quality of the products in their pipelines. That's what determines if they are going to have sustainable revenues and earnings. It's also why so many Analysts on The Street pay such close attention to FDA pronouncements.

3. What kinds of metrics would you gauge to determine the financial, strategic and operational health of a prospective alliance partner?

Several metrics are available in each sector you mention. To gauge the financial health of a prospective partner, I would look at product sales growth or I might look at whether they've met their milestones. To gauge strategic health, I'd consider their market share growth or, how well their customers have access to the company. For operational health, I'd again look to see whether they've met their milestones, how well they make decisions as gauged by the rating we give them and how quickly they resolve conflicts. Good evaluations in these areas suggest that the prospective alliance will be viable for both parties.

What are the limitations of blotting techniques and what alternatives can you suggest?

The major limitation of blotting procedures is the length of time needed and the fact that they can accommodate only one probe at a time.

What technique is used to measure the number of copies of a gene or an RNA molecule in human tissues?

PCR or polymerase chain reaction in real time, as opposed to the conventional method, because the number of copies of the target molecule can be monitored for each PCR cycle.

What is a Living Modified Organism (LMO)?

State one other desirable feature which could be genetically engineered into crop plants.

Name the bacterium from which the Bt gene is isolated.

What feature of monoclonal antibodies makes them useful for biochemical testing?

Other than forensic DNA fingerprinting, state another application of this DNA profiling technology.

What should be included on the gel to enable you to determine actual sizes of the DNA fragments?

State two advantages of using immobilised enzymes.

What term is used to describe animals which have had their genome altered by recombinant DNA technology?

Injecting live viruses to stimulate the production of antibodies is which type of immunity?

Describe how you would determine the number of viruses present.

Name the dye commonly used as the counterstain in the Gram staining process.

What kinds of metrics would you gauge to determine the financial, strategic and operational health of a prospective alliance partner?

How would you value a biotech company as opposed to a consumer products company?

How to run DOCK 6 using cygwin?

Explain Homology modelling?



Computational Biology (2)



Computational Biology (3)



Computational Biology (4)



1.When a bicycle is in motion, the force of friction exerted by the ground on the two wheels is such that it acts

(a) In the backward direction on the front wheel and in the forward direction on the rear wheel.
(b) In the forward direction on the front wheel and in the backward direction on the rear wheel.
© In the backward direction on both the front and rear wheels.
(d) In the backward direction on both the front and rear wheels.

d) In the backward direction on both the front and rear wheels.

2. A certain radioactive element A, has a half life = t seconds. In (t/2) seconds the fraction of the initial quantity of the element so far decayed is nearly

(a) 29%
(b) 15%
© 10%
(d) 45%

(a) 29%

3. Which of the following plots would be a straight line ?

(a) Logarithm of decay rate against logarithm of time
(b) Logarithm of decay rate against logarithm of number of decaying nuclei
© Decay rate against time
(d) Number of decaying nuclei against time

(b) Logarithm of decay rate against logarithm of number of decaying nuclei

4. A radioactive element x has an atomic number of 100. It decays directly into an element y which decays directly into element z. In both processes a charged particle is emitted. Which of the following statements would be true?

(a) y has an atomic number of 102
(b) y has an atomic number of 101
© z has an atomic number of 100
(d) z has an atomic number of 101

(b) y has an atomic number of 101

5. If the sum of the roots of the equation ax2 + bx + c=0 is equal to the sum of the squares of their reciprocals then a/c, b/a, c/b are in

(a) AP
(b) GP
© HP
(d) None of these

© HP

6. A man speaks the truth 3 out of 4 times. He throws a die and reports it to be a 6. What is the probability of it being a 6?

(a) 3/8
(b) 5/8
© 3/4
(d) None of the above

(a) 3/8

7. If cos2A + cos2B + cos2C = 1 then ABC is a

(a) Right angle triangle
(b) Equilateral triangle
© All the angles are acute
(d) None of these

(a) Right angle triangle

8. Image of point (3,8) in the line x + 3y = 7 is

(a) (-1,-4)
(b) (-1,4)
© (2,-4)
(d) (-2,-4)

(a) (-1,-4)

9. The mass number of a nucleus is

(a) Always less than its atomic number
(b) Always more than its atomic number
© Sometimes more than and sometimes equal to its atomic number
(d) None of the above

© Sometimes more than and sometimes equal to its atomic number

10. The maximum KE of the photoelectron emitted from a surface is dependent on

(a) The intensity of incident radiation
(b) The potential of the collector electrode
© The frequency of incident radiation
(d) The angle of incidence of radiation of the surface

© The frequency of incident radiation

11. Which of the following is not an essential condition for interference

(a) The two interfering waves must be propagated in almost the same direction or the two interfering waves must intersect at a very small angle
(b) The waves must have the same time period and wavelength
© Amplitude of the two waves should be the same
(d) The interfering beams of light must originate from the same source

© Amplitude of the two waves should be the same

12. When X-Ray photons collide with electrons

(a) They slow down
(b) Their mass increases
© Their wave length increases
(d) Their energy decreases

© Their wave length increases

13. An electron emits energy

(a) Because its in orbit
(b) When it jumps from one energy level to another
© Electrons are attracted towards the nucleus
(d) The electrostatic force is insufficient to hold the electrons in orbits

(b) When it jumps from one energy level to another

14. How many bonds are present in CO2 molecule?

(a) 1
(b) 2
© 0
(d) 4

(d) 4

15. In a balanced chemical equation

(a) Atoms are conserved
(b) Molecules are conserved
© Moles are conserved
(d) Reactant and product molecules are preserved

(a) Atoms are conserved

16. How many grams of NaOH will react with 0.2 equivalent of HCl?

(a) 0.59
(b) 0.285
© 1.18
(d) none of these

(a) 0.59

17. Which of the following is least acidic

(a) Ortho-cresol
(b) Para-cresol
© Phenol
(d) Meta-cresol

(b) Para-cresol

18. In Reimer-Tiemann’s reaction, the reaction intermediate is

(a) Carbene
(b) Dichloro carbene
© Carbonion
(d) Carbonium ion

(b) Dichloro carbene

19. Which of the following is most acidic?

(a) C2H5OH
(b) CH3CHOHCH3
© Ethanol
(d) CH3OH

(b) CH3CHOHCH3

20.A catalyst

(a)always slows down the reaction
(b)always starts a rection that would not have ocurred at all otherwise
©causes changes in the rate of the reaction
(d)changes the quantities of the products formed

©causes changes in the rate of the reaction

21.The rate of the first order reaction depends on the

(a) Concentration of the reactant
(b) Concentration of the product
© Time
(d) Temperature

(d) Temperature

22. The most abundant element in the universe is

(a) Hydrogen
(b) Helium
© Oxygen
(d) Silicon

(a) Hydrogen

23. Integrate 3x + 5 / (x3-x2-x+1)

(a) 1/2 log | (x+1)/(x-1) | - 4/(x-1)
(b) log |2+tanx|
© -(1+logx)/x
(d) 2 log|(tanx)/(tanx+2)

(a) 1/2 log | (x+1)/(x-1) | - 4/(x-1)

24. If y=cos-1(cosx + 4sinx)/(17)1/2, then dy/dx is

(a) 0
(b) 1
©-1
(d) none of these

(b) 1

25. If the sum of n terms of two series of A.P are in the ratio 5n+4:9n+6 .find the ratio of their 13th terms

(a) 129/231
(b) 1/2
© 23/15
(d) None of the above

(a) 129/231

26. If the letters of the word “rachit” are arranged in all possible ways and these words are written out as in a dictionary, what is the rank of the word “rachit”.

(a) 485
(b) 480
© 478
(d) 481

(d) 481

27. Ravi’s salary was reduced by 25%.Percentage increase to be effected to bring the salary to the original level is (a) 20% (b) 25% © 33 1/3% (d) 30%

© 33 1/3%

28. A and B can finish a piece of work in 20 days .B and C in 30 days and C and A in 40 days. In how many days will A alone finish the job

(a) 48
(b) 34 2/7
© 44
(d) 45

(a) 48

29. How long will a train 100m long traveling at 72kmph take to overtake another train 200m long traveling at 54kmph

(a) 70sec
(b) 1min
© 1 min 15 sec
(d) 55 sec

(b) 1min

30. What is the product of the irrational roots of the equation (2x-1)(2x-3)(2x-5)(2x-7)=9? (a) 3/2 (b) 4 © 3 (d) 3/4

(a) 3/2

31. Which of the following parameters is the same for molecules of all gases at a given temperature?

(a) Mass
(b) Momentum
© Speed
(d) Kinetic energy

(d) Kinetic energy

32. A solid is completely immersed in liquid. The force exerted by the liquid on the solid will

(a) Increase if it is pushed deeper inside the liquid
(b) Change if its orientation is changed
© Decrease if it is taken partially out of the liquid
(d) None of the above

© Decrease if it is taken partially out of the liquid

33. Select the correct statements

(a) A simple harmonic motion is necessarily periodic
(b) An oscillatory motion is necessarily periodic
© A periodic motion is necessarily oscillatory
(d) All of the above

(a) A simple harmonic motion is necessarily periodic

34. An electron is injected into a region of uniform magnetic flux density with the components of velocity parallel to and normal to the flux. What is the path of the electron?

(a) Helix
(b) Parabola
© Circle
(d) Rectangle

(a) Helix

35. A constant voltage is applied between the 2 ends of a uniform metallic wire. Some heat is developed in it. The heat developed is doubled if

(a) both the length and radius of the wire are halved.
(b) both the length and radius of the wire are doubled
© the radius of the wire is doubled
(d) the length of the wire is doubled

(b) both the length and radius of the wire are doubled

36. If Young’s double slit experiment is performed in water

(a) the fringe width will decrease
(b) the fringe width will increase
© the fringe width remains unchanged
(d) there will be no fringe

(a) the fringe width will decrease

37. The shape of a spot of light produced when bright sunshine passes perpendicular through a hole of very small size is (a) Square, because the hole is a square (b) Round, because it is an image of the sun © Round with a small penumbra around it (d) Square with a small penumbra

(b) Round, because it is an image of the sun

38. Some forms are books. All books are made of paper

(a) Some forms are made of paper
(b) Some forms are not made of paper
© No forms are made of paper
(d) None of the above

(a) Some forms are made of paper

39. All toffees are chocolates. Some toffees are not good for health. (a) Some chocolates are not good for health (b) Some toffees are good for health © No toffees are good for health (d) Both (a) and (b)

(a) Some chocolates are not good for health

The questions 40-46 are based on the following pattern.The problems below contain a question and two statements giving certain data. You have to decide whether the data given in the statements are sufficient for answering the questions.The correct answer is

(A) If statement (I) alone is sufficient but statement (II) alone is not sufficient
. (B) If statement(II) alone is sufficient but statement(I) alone is not sufficient.
© If both statements together are sufficient but neither of statements alone is sufficient.
(D) If both together are not sufficient.
(E) If statements (I) and (II) are identical.

43. If a ground is rectangular, what is its width?

(I) The ratio of its length to its breadth is 7:2
(II) Perimeter of the playground is 396 mts.

© If both statements together are sufficient but neither of statements alone is sufficient.

44. If the present age of my father is 39 yrs and my present age is x yrs, what is x?

(I) Next year my mother will be four times as old as i would be.
(II) My brother is 2 years older than I and my father is 4 years older than my mother.

© If both statements together are sufficient but neither of statements alone is sufficient.

45. How many brothers and sisters are there in the family of seven children?

(I) Each boy in the family has as many sisters as brothers
(II) Each of the girl in the family has twice as many brothers as sisters

(D) If both together are not sufficient.

46. x is not equal to 0, is x + y = 0? (I) x is the reciprocal of y (II) x is not equal to 1

(A) If statement (I) alone is sufficient but statement (II) alone is not sufficient.

47. ? : BGLQ : : YDIN : VAFK

(a) EKNS
(b) DKMT
© DLMS
(d) EJOT

(d) EJOT

48. NLO : RPS : : ? : ZXA

(a) VUW
(b) VTR
© VTW
(d) TRP

© VTW

49. If “segment” is coded as rffndou, then “ritual” is coded as

(a) shutbm
(b) qjutbk
© qhutbk
(d) qhubtk

© qhutbk

50. If “football” is “cricket” ,”cricket” is “basketball” ,”basketball” is “volleyball”,”volleyball” is “khokho” and “khokho” is cricket, which is not a ball game? (a) cricket (b) football © khokho (d) basketball

(a) cricket

51. Which of the following is a recursive set of production

(a) S –> a|A, A –> S
(b) S –> a|A, A –> b
© S –>aA, A–>S
(d) None of these

© S –>aA, A–>S

User Study during Bioinformatics course: Interview questions
User groups: natural science students, chemistry students, molecular life science students, PhD’s of CMBI

Why are you interested in bioinformatics?

What are your main research interests?

Did you work on any group projects/ assignments? What was the assignment about? How did you assign the tasks in the group?

Could you think of a research task where work in a group could be beneficial?

Did you use any bioinformatics tools before?
a. If yes:
i. Which tools?
ii. How frequently?
iii. In what experiments, how did you use them?

Are you planning to use bioinformatics tools after the course?
b. If yes, for what purpose/experiments?
c. If no, why?
i. Do you see benefits in using these tools for the research purposes?
ii. Do you see benefits/long-term benefits in putting an effort now and later in learning these tools?

Do you think that if using these tools for scientific purposes they could lead you to the new research questions/provide you with innovative knowledge in an efficient way?

What are the important aspects you think these tools should support? (<- for the questionnaire may be ask participants to rate items)
d. motivation
e. creativity
f. personalization [1]
g. collaboration between scientists
h. group work
i. support during the whole experiment flow
j. reliability of the output
k. trust

Have you ever used/seen one o the workflow systems? (<-may be only for PhD’s)
l. Taverna
m. Kepler
n. Triana
If yes, what did you think, are they useful?