Answer to Question #154911 in Bioinformatics for Vaibhav

Question

(a) Explain sensitivity and selectivity in terms of true and false positives.

(b) What is the advantage of a Needleman-Wunsch alignment compared to a seeded alignment?

(c) What does the expectation parameter mean in local alignment? What will happen if the expectation value is increased from its default value of 10 to a 100?

Answer 1

a) Sensitivity measures the amount or proportion of positive that are identified correctly. If a model or test incorrectly predicts the positive result as negative it is called false positive and the correct prediction of positive called a true positive. 

Specificity likewise this models measure of how well a test can identify true negatives. False-negative is when the models identified negative results as positive. 

b) The global (Needleaman and Wunsch ) alignment technique aligns a sequence end to end, the entire sequence from start to end, hence it is used in a homologous gene or protein comparison in different species. 

(c) Whereas local seeded alignment like BLAST is more advantageous over global alignment because it aligns sequences with the highest level of similarities and because of that it is used in conserved sequence alignment study.