Bioinformatics Practice Test 2

1. Which of the following is incorrect regarding sequence homology?

When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship

Two sequences can homologous relationship even if have do not have common origin

When two sequences are descended from a common evolutionary origin, they are said to share homology

It is an important concept in sequence analysis

2. Which of the following is not a drawback of the progressive alignment method?

The final alignment result is also influenced by the order of sequence addition

In this method the use of affine gap penalties, long gaps is allowed, and, in some cases, this may limit the accuracy of the method

The progressive alignment method is not suitable for comparing sequences of different lengths because it is a global alignment–based method

In this method the use of affine gap penalties, long gaps are not allowed, and, in some cases, this may limit the accuracy of the method

3. The second step in the Genetic Algorithm comprises of scoring of the 100 initial MSAs by the sum of pairs method.

False

True

4. The statistical analysis of alignment scores is much better understood for ________ than for _______

global alignments, any other alignment method

global alignments, local alignments

local alignments, global alignments

Needleman-Wunsch alignment, Smith-Waterman alignment

5. As the amount of computational time and memory space required increases exponentially with the number of sequences, it makes the multidimensional search matrix method computationally prohibitive to use for a large data set.

False

True

6. A length and distance that gives the highest overall probability may then be determined. Such alignments are initially found using ________

an alignment algorithm and a particular scoring matrix

dot method

a particular scoring matrix only

an alignment algorithm only

7. Sequence similarity and sequence identity are synonymous for nucleotide sequences and protein sequences as well.

False

True

8. The global sequence alignment is suitable when the two sequences are of dissimilar length, with a negligible degree of similarity throughout.

False

True

9. Shorter sequences require higher cutoffs for inferring homologous relationships than longer sequences.

True

False

10. Which of the following is untrue about PILEUP program?

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

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

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