Question

Which of the following is untrue about PILEUP program?

(a) It is the MSA program that is a part of the Genetics Computer Group package of sequence analysis programs

(b) It is owned since 1997 by Oxford Communications and is widely used due to the popularity and availability of this package

(c) It uses a method for MSA that is polar opposite to CLUSTALW

(d) The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm

I have been asked this question in semester exam.

Enquiry is from Progressive Methods of Multiple Sequence Alignment topic in chapter Multiple Sequence Alignment of Bioinformatics

Answer 1

Right option is (c) It uses a method for MSA that is polar opposite to CLUSTALW

Best explanation: PILEUP uses a method for MSA that is very similar to CLUSTALW. The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm, and the scores are used to produce a tree by the unweighted pair-group method using arithmetic averages. The resulting tree is then used to guide the alignment of the most closely related sequences and groups of sequences. The resulting alignment is a global alignment produced by the Needleman-Wunsch algorithm.