Bioinformatics Interview Questions and Answers

1 :: How do you customise database for blast?

Step 1. Assemble your sequences.

Put all your sequences in Fasta format in a single file.
This file should be located in a suitably named
subdirectory of your home directory on the UBiC Blast
server. The definition line for each sequence should start
with a unique identifier for that sequence.

Step 2. Convert this sequence file to a Blastable database.

The command formatdb converts your Fasta file of sequences
to a set of files that can be queried with command-line
BLAST.

Step 3. Test Blast on your database.


See the UBiC tutorial, Using Command-line BLAST. In the
blastall command-line you will need to specify the location
of your database by typing: -
d /disk2/home/myhome/blastdbs/custom.aa.

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2 :: How much template do you need for sequencing?

For PCR product size of product(bp)/50 = ng DNA. For plasmid up to 10.0 kb 250-300 ng. For genomic DNA 2.0 microgram.

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3 :: What is a clean and run reaction?

This means that purchase a BigDye terminator kit from our facility and run the cycle sequencing reaction and post clean-up. We recommend using Princeton Separations Centri-Sep spin columns or Abgene Dye Terminator Removal Plates.
Drop off your sample in the form of a dried pellet in 1.5 ml eppendorf tube along with your request form. Your dnalims request order will have Seq_Drop_Off selected under Service Requested, and have no selected under Spin-Column Clean-up.

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4 :: How did you get into the field of bioinformatics?

My background is in computer sciences, including design of algorithms and theoretical computer science. I got interested in this because of some work in an area called DNA computing. That idea is to build computers out of DNA. The person who started that line of work - is a computer scientist who spent a quite a bit of time in a biology lab. His work really caught the attention of many people in the computer science community. But then, as I got more interested in some of the algorithmic problems that come up, I realized they are also relevant in the more traditional biological areas. You have to talk to chemists and biochemists if you want to understand DNA and RNA - you can’t get the right level of understanding just from reading papers. I got more interested in their perspectives and problems.

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5 :: Tell us about three kinds of DNA?

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.

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