![Q.39 Determine the correctness or otherwise of the following Assertion [a] and the Reason [r] Assertion: Ab initio gene finding algorithms that predict protein coding genes in eukaryotic genomes are not completely accurate. Reason: Eukaryotic splice sites are difficult to predict. (A) Both [a] and [r] are false (B) [a] is true but [r] is false (C) Both [a] and [r] are true and [r] is the correct reason for [a] (D) Both [a] and [r] are true but [r] is not the correct reason for [a]](https://www.letstalkacademy.com/wp-content/uploads/2026/01/slide_39-12.png)
Q.39 Determine the correctness or otherwise of the following Assertion [a] and the Reason [r]
Assertion: Ab initio gene finding algorithms that predict protein coding genes in eukaryotic
genomes are not completely accurate.
Reason: Eukaryotic splice sites are difficult to predict.
(A) Both [a] and [r] are false
(B) [a] is true but [r] is false
(C) Both [a] and [r] are true and [r] is the correct reason for [a]
(D) Both [a] and [r] are true but [r] is not the correct reason for [a]
Ab initio gene finding algorithms struggle to achieve perfect accuracy in predicting eukaryotic protein-coding genes. The correct answer is option (C): Both [a] and [r] are true, and [r] is the correct reason for [a].
Why Assertion [a] Is True
Ab initio algorithms rely on statistical models and sequence features like codon usage and open reading frames to predict genes without external evidence. Eukaryotic genomes pose unique challenges, including complex intron-exon structures, alternative splicing, and regulatory elements, resulting in accuracies often below 80% at the exon level. Benchmark studies confirm top tools like Augustus and GeneScan reach only 50-76% accuracy depending on organism clades.
Why Reason [r] Is True
Eukaryotic splice sites feature degenerate consensus sequences like GT-AG, with weak signals amid high genomic noise, making precise donor and acceptor site prediction error-prone. Tools like NNSPLICE score sites probabilistically, but false positives/negatives persist due to variability across species and tissues.
Option-by-Option Breakdown
| Option | Correctness | Explanation |
|---|---|---|
| (A) Both false | Incorrect | Contradicts evidence of inaccuracy in ab initio predictions and splice site challenges. |
| (B) [a] true, [r] false | Incorrect | [r] holds as splice prediction remains difficult despite advances. |
| (C) Both true, [r] explains [a] | Correct | Splice site errors directly cause frequent exon boundary misses, core to ab initio limitations in eukaryotes. |
| (D) Both true, [r] unrelated | Incorrect | Other issues exist (e.g., UTRs, promoters), but splice prediction is a primary reason for inaccuracy. |
