Bioinformatics Practice Test 1

1. Which of the following does not describe local alignment?

The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global

A local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score

Local alignments have terminal gaps

A local alignment aligns a substring of the query sequence to a substring of the target sequence

2. Vertical frame shifts show ______ while the horizontal ones show _______

deletion, insertion

insertion, deletion

deletion, deletion

insertion, insertion

3. While scanning for similarities in motifs, how regular expressions’ techniques work?

Dot matrix analysis is used in this type of sequence analysis

An algorithm similar to dynamic programming is used

It represents a sequence family by a string of characters and further compares them

Matrix analysis methods are used in this type

4. Which of the following is untrue in case of the database BLOCKS?

The alignments are automatically generated using the same data sets used for deriving the BLOSUM matrices

The functional annotation of blocks is not consistent with that for the motifs

A weighting scheme and pseudo counts are subsequently applied to the PSSMs to account for underrepresented and unobserved residues in alignments

The derived ungapped alignments are called ‘blocks’, which are usually longer than motifs, are subsequently converted to PSSMs

5. Which of the following does not describe BLOSUM matrices?

It stands for BLOcks SUbstitution Matrix

These matrices are logarithmic identity values

The year it was developed was 1992

It was developed by Henikoff and Henikoff

6. Gaps are added to the alignment because it ______

increases the matching of or dissimilar amino acids at subsequent portions in the alignment

increases the matching of identical amino acids at subsequent portions in the alignment

reduces the overall score

enhances the area of the sequences

7. When did Smith–Waterman first describe the algorithm for local alignment?

1925

1950

1970

1981

8. Who were the inventors of this method?

Needleman-Wunsch

Margaret Preston

Gibbs and McIntyre

Smith-Waterman

9. For palindromic sequences, what is the structure of the dot plot?

2 intersecting diagonal lines at the midpoint

No diagonal

Two parallel diagonals

One diagonal

10. Which of the following least describes Long Loop β-hairpins?

Loop looks similar to the Greek Letter Ω

They are Often referred to as a 'random coil' conformation

Wide-range of conformations with very specific sequence preferences

Generally they are referred to as the β-meander supersecondary structure