Bio Informatics Interview Questions and Answers

1 :: Suppose you used the NCBI Blast server to look for a match to a fruit-fly gene.

Suppose further that the best alignment contained this
section of an alignment:

Hit from database: XXXXXXXXXXXXXXNFSTSQ

user sequence: SLEAEAAPASISPSNFSSSQ
What do the Xs signify?

unknown amino acid

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2 :: How you calculate sensitivity and selectivity of Blast?

Suppose the Blast search returned 100 hits. Of these, 17
were false positives and we knew that there were 165
sequences in

the database which should have returned a hit with our
sequence.


To calculate the sensitivity and selectivity, we must
determine the number of true positives (ntp), the number of
false

positives (nfp) and the number of false negatives (nfn). We
are told that the number of false positives was 17, hence
the

number true positives must have been 100-17 = 83, as there
were 100 hits. Therefore we know that the search algorithm
found

83 of the 165 sequences it should have found, hence the
number of false negatives was 165-83 = 82. So, we know that
ntp = 83,

nfp = 17 and nfn=82. Using the equations in the notes, we
can calculate:

Sensitivity = ntp/(ntp+nfn) = 83/(83+82) = 83/165 = 0.50 (2
d.p)

Selectivity = ntp/(ntp+nfp) = 83/(83+17) = 83/100 = 0.83

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3 :: What are the main approaches of predicting protein interactions using genomic context analysis?

We have developed an approach using Bayesian networks to
predict protein-protein interactions genome-wide in yeast.
Our method naturally weights and combines into reliable
predictions genomic features only weakly associated with
interaction (e.g., messenger RNAcoexpression,
coessentiality, and colocalization). In addition to de novo
predictions, it can integrate often noisy, experimental
interaction data sets. We observe that at given levels of
sensitivity, our predictions are more accurate than the
existing high-throughput experimental data sets

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4 :: What is the main idea of maximum parsimony in phylogenetic tree construction? What are the drawbacks?

The Maximum Parsimony (MP) problem aims at reconstructing a
phylogenetic tree from DNA sequences while minimizing the
number of genetic transformations. To solve this NP-
complete problem, heuristic methods have been developed,
often based on local search. In this paper, we focus on the
influence of the neighborhood relations

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5 :: Which of the following sequences contains the pattern [AG]-x
(4)-G-K-[ST] from the PROSITE database?

seq. A: VAGWGKST
seq B: GVLKRGKS
seq. C: AGVLKGRT
seq. D: AGVGKSTP?

seq. C: AGVLKGRT

[AG]-x (4)-G-K-[ST]
decodin the pattern:
A or G in the first position,(note both sequence C and D
start with the same)
X any amino acid follows the next four positions (2-5)
G in the sixth position (note seq C alone satify)
k in the seventh position
S or T in the eigth position (note seq C alone satify)

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