Question

Which of the following is incorrect regarding the Prediction for Eukaryotes?

(a) The consensus patterns are only derived from bioinformatics studies

(b) The experimentally determined DNA binding sites are compiled into profiles and stored in a database for scanning an unknown sequence to find similar conserved patterns

(c) The consensus patterns are derived from experimentally determined DNA binding sites

(d) The ab initio method for predicting eukaryotic promoters and regulatory elements relies on searching the input sequences for matching of consensus patterns of known promoters and regulatory elements

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I'm obligated to ask this question of Prediction Algorithms topic in section Promoter and Regulatory Element Prediction of Bioinformatics

Answer 1

Correct answer is (a) The consensus patterns are only derived from bioinformatics studies

The explanation is: This approach tends to generate very high rate of false positives owing to nonspecific matches with the short sequence patterns. Furthermore, because of the high variability of transcription factor binding sites, the simple sequence matching often misses true promoter sites, creating false negatives.