Bioinformatics Interview Questions and Answers

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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.

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