Question

Which of the following is untrue about EST2Genome?

(a) It is a web-based program purely based on the sequence alignment approach to define intron–exon boundaries

(b) It compares an EST (or cDNA) sequence with a genomic DNA sequence containing the corresponding gene

(c) The alignment is rarely done using a dynamic programming–based algorithm

(d) Advantage of the approach is the ability to find very small exons and alternatively spliced exons that are very difficult to predict by any ab initio–type algorithms

I got this question in a national level competition.

Query is from Gene Prediction in Eukaryotes topic in portion Gene and Promoter Prediction of Bioinformatics

Answer 1

Right choice is (c) The alignment is rarely done using a dynamic programming–based algorithm

To explain I would say: The alignment is done using dynamic programming–based algorithm. Another advantage is that there is no need for model training, which provides much more flexibility for gene prediction. The limitation is that EST or cDNA sequences often contain errors or even introns if the transcripts are not completely spliced before reverse transcription.