• Sequence alignment includes calculating the so-called edit distance, which generally corresponds to the minimal number of substitutions, insertions, and
deletions needed to turn one sequence into another.
• The choice of a sequencing read alignment tool depends on your goals and the
specific case.
Review Questions
1. Assume you are performing a mapping with STAR. After the process, where do you
find the information how many reads have mapped only at one position of the
reference genome?
2. Which of the following does not describe local alignment?
A. A local alignment aligns a substring of the query sequence to a substring of the
target sequence.
B. 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.
C. Local alignments have terminal gap.
D. 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.
3. Which of the following does not describe BLAST?
A. It stands for Basic Local Alignment Search Tool.
B. It uses word matching like FASTA.
C. It is one of the tools of the NCBI.
D. Even if no words are similar, there is an alignment to be considered.
4. Which of the following does not describe dynamic programming?
A. The approach compares every pair of characters in the two sequences and
generates an alignment, which is the best or optimal.
B. Global alignment algorithm is based on this method.
C. Local alignment algorithm is based on this method.
D. The method can be useful in aligning protein sequences to protein sequences
only.
5. Which of the following is not a disadvantage of Needleman–Wunsch algorithm?
A. This method is comparatively slow.
B. There is a need of intensive memory.
C. This cannot be applied on genome sized sequences.
D. This method can be applied to even large sized sequences.
6. Alignment algorithms, both global and local, are fundamentally similar and only
differ in the optimization strategy used in aligning similar residues.
A. True.
B. False.
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deletions needed to turn one sequence into another.
• The choice of a sequencing read alignment tool depends on your goals and the
specific case.
Review Questions
1. Assume you are performing a mapping with STAR. After the process, where do you
find the information how many reads have mapped only at one position of the
reference genome?
2. Which of the following does not describe local alignment?
A. A local alignment aligns a substring of the query sequence to a substring of the
target sequence.
B. 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.
C. Local alignments have terminal gap.
D. 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.
3. Which of the following does not describe BLAST?
A. It stands for Basic Local Alignment Search Tool.
B. It uses word matching like FASTA.
C. It is one of the tools of the NCBI.
D. Even if no words are similar, there is an alignment to be considered.
4. Which of the following does not describe dynamic programming?
A. The approach compares every pair of characters in the two sequences and
generates an alignment, which is the best or optimal.
B. Global alignment algorithm is based on this method.
C. Local alignment algorithm is based on this method.
D. The method can be useful in aligning protein sequences to protein sequences
only.
5. Which of the following is not a disadvantage of Needleman–Wunsch algorithm?
A. This method is comparatively slow.
B. There is a need of intensive memory.
C. This cannot be applied on genome sized sequences.
D. This method can be applied to even large sized sequences.
6. Alignment algorithms, both global and local, are fundamentally similar and only
differ in the optimization strategy used in aligning similar residues.
A. True.
B. False.
9 Alignment
121