Which of the following is untrue about PILEUP program?

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

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

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

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

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

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1.	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.
A.	True
B.	False
Answer» B. False

Discussion

2.	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
Answer» D. The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm

Discussion

3.	Like other alignment programs, CLUSTAL uses a null score for opening a gap in a sequence alignment and a penalty for extending the gap by one residue.
A.	True
B.	False
Answer» C.

Discussion

4.	The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment.
A.	True
B.	False
Answer» B. False

Discussion

5.	Progressive alignment methods use the dynamic programming method to build an MSA starting with the most related sequences and then progressively adding less related sequences or groups of sequences to the initial alignment.
A.	True
B.	False
Answer» B. False

Discussion

Explore topic-wise MCQs in Bioinformatics.

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.

Which of the following is untrue about PILEUP program?

Like other alignment programs, CLUSTAL uses a null score for opening a gap in a sequence alignment and a penalty for extending the gap by one residue.

The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment.

Progressive alignment methods use the dynamic programming method to build an MSA starting with the most related sequences and then progressively adding less related sequences or groups of sequences to the initial alignment.