7. The function of the scoring matrix is to conduct one-to-one comparisons between all
components in two sequences and record the optimal alignment results.
A. True.
B. False.
Answers to Review Questions
1. Log.final.out in the output directory of alignment file (.bam); 2. C; 3. D; 4. D; 5. D; 6.
A; 7. A
Acknowledgements We are grateful to Dr. Richa Bharti (Bioinformatician at TUM Campus
Straubing, Germany) and Dr. Philipp Torkler (Senior Bioinformatics Scientist, Exosome Diagnostics,
a Bio-Techne brand, Munich, Germany) for critically reading this text. We thank for correcting our
mistakes and suggesting relevant improvements to the original manuscript.
References
1. Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc
Natl Acad Sci U S A. 1983;80(3):726–30.
2. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci
U S A. 1988;85(8):2444–8.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol
Biol. 1990;215(3):403–10.
4. Canzar S, Salzberg SL. Short read mapping: an algorithmic tour. Proc IEEE Inst Electr Electron
Eng. 2017;105(3):436–58.
5. Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing
data. Bioinformatics. 2012;28(24):3169–77.
6. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the
amino acid sequence of two proteins. J Mol Biol. 1970;48(3):443–53.
7. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol.
1981;147(1):195–7.
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009;25(14):1754–60.
9. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.
Bioinformatics. 2010;26(5):589–95.
10. Dobin A, Gingeras TR. Optimizing RNA-seq mapping with STAR. Methods Mol Biol.
2016;1415:245–62.
11. Langmead B. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics.
2010;32:11–7.
12. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short
DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
13. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9
(4):357–9.
14. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of
transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):
R36.
15. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements.
Nat Methods. 2015;12(4):357–60.
122
M. Kappelmann-Fenzl
components in two sequences and record the optimal alignment results.
A. True.
B. False.
Answers to Review Questions
1. Log.final.out in the output directory of alignment file (.bam); 2. C; 3. D; 4. D; 5. D; 6.
A; 7. A
Acknowledgements We are grateful to Dr. Richa Bharti (Bioinformatician at TUM Campus
Straubing, Germany) and Dr. Philipp Torkler (Senior Bioinformatics Scientist, Exosome Diagnostics,
a Bio-Techne brand, Munich, Germany) for critically reading this text. We thank for correcting our
mistakes and suggesting relevant improvements to the original manuscript.
References
1. Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc
Natl Acad Sci U S A. 1983;80(3):726–30.
2. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci
U S A. 1988;85(8):2444–8.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol
Biol. 1990;215(3):403–10.
4. Canzar S, Salzberg SL. Short read mapping: an algorithmic tour. Proc IEEE Inst Electr Electron
Eng. 2017;105(3):436–58.
5. Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing
data. Bioinformatics. 2012;28(24):3169–77.
6. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the
amino acid sequence of two proteins. J Mol Biol. 1970;48(3):443–53.
7. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol.
1981;147(1):195–7.
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009;25(14):1754–60.
9. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.
Bioinformatics. 2010;26(5):589–95.
10. Dobin A, Gingeras TR. Optimizing RNA-seq mapping with STAR. Methods Mol Biol.
2016;1415:245–62.
11. Langmead B. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics.
2010;32:11–7.
12. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short
DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
13. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9
(4):357–9.
14. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of
transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):
R36.
15. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements.
Nat Methods. 2015;12(4):357–60.
122
M. Kappelmann-Fenzl