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Which of the following is incorrect about Phrap?(a) It aligns individual fragments in a pairwise fashion using the Smith–Waterman algorithm(b) It doesn’t take input from Phred(c) It is used for sequence assembly(d) It is a UNIX programThe question was posed to me in homework.This interesting question is from Genome Sequence Assembly in chapter Genome Mapping, Assembly and Comparison of Bioinformatics

Answer»

Correct answer is (B) It doesn’t take input from Phred

For explanation: It takes Phred BASE-call files with quality scores as input and aligns individual fragments in a pairwise fashion USING the Smith–Waterman algorithm. The base quality information is taken into account during the pairwise alignment. After all the pair wise sequence similarity is identified, the program performs assembly by progressively merging sequence pairs with decreasing similarity scores while removing overlapped regions. Consensus contigs are DERIVED after joining all possible overlapped READS.



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