Index
A
Adapter ligation, 41
Adoptive T-cell therapy, 29
Alignment
algorithms, 112
BLAST program, 113
computer science, 112
FASTA program suite, 113
global alignment, 114, 115
local alignment, 115, 116
Needleman–Wunsch alignment, 114
reference genome/transcriptome, 112
sequence alignment software tools, 113
sequence databases, 113
Alignment tools
Bowtie2, 118
BWA, 119
HISAT, 120
HISAT2, 120
STAR, 117
TopHat aligns RNA-Seq reads, 119
American College of Medical Genetics and
Genomics (ACMG), 21
Amino acid (AA), 6
Antibodies, 179
Aplice-aware alignment tools, 150
Aristolactam-DNA adducts, 23
B
BAM file, 86, 87
Base calling, 124, 129, 139
Bash (bourne-again shell), 72
Bayesian variant calling, 126–128
BeadArray Microarray Technology, 48
BED format, 88, 89
BedGraph (*.bg) format, 90
BedTools, 187
BEDTools commands, 90
BET and MEK inhibitors, 29
Beta allele frequency (BAF), 184
Big data, 48
Binary base call (BCL), 49
Binding motifs, 178
BiocManager, 67
Bioconda, 62–64, 68
Bioconductor, 67
Bioinformatics, 72
Biological ontology method, 168
Biological sequence variants, 48
Biological sequences
DNA (see Deoxyribonucleic acid (DNA))
genome, 6
protein, 6
BLAST program, 113
Bowtie, 118
Bowtie2, 118
Bowtie2 alignment tools, 108
BRAF inhibitors, 28, 30
Breast cancer, 29
Bulk genome sequencing, 33
Bulk transcriptome sequencing, 28
Burrow–Wheeler Aligner (BWA), 119
C
Cancer
cause of death, 18
DNA binding domain, 20
genome disease, 18
mutations, 18
research, 18
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3
211
A
Adapter ligation, 41
Adoptive T-cell therapy, 29
Alignment
algorithms, 112
BLAST program, 113
computer science, 112
FASTA program suite, 113
global alignment, 114, 115
local alignment, 115, 116
Needleman–Wunsch alignment, 114
reference genome/transcriptome, 112
sequence alignment software tools, 113
sequence databases, 113
Alignment tools
Bowtie2, 118
BWA, 119
HISAT, 120
HISAT2, 120
STAR, 117
TopHat aligns RNA-Seq reads, 119
American College of Medical Genetics and
Genomics (ACMG), 21
Amino acid (AA), 6
Antibodies, 179
Aplice-aware alignment tools, 150
Aristolactam-DNA adducts, 23
B
BAM file, 86, 87
Base calling, 124, 129, 139
Bash (bourne-again shell), 72
Bayesian variant calling, 126–128
BeadArray Microarray Technology, 48
BED format, 88, 89
BedGraph (*.bg) format, 90
BedTools, 187
BEDTools commands, 90
BET and MEK inhibitors, 29
Beta allele frequency (BAF), 184
Big data, 48
Binary base call (BCL), 49
Binding motifs, 178
BiocManager, 67
Bioconda, 62–64, 68
Bioconductor, 67
Bioinformatics, 72
Biological ontology method, 168
Biological sequence variants, 48
Biological sequences
DNA (see Deoxyribonucleic acid (DNA))
genome, 6
protein, 6
BLAST program, 113
Bowtie, 118
Bowtie2, 118
Bowtie2 alignment tools, 108
BRAF inhibitors, 28, 30
Breast cancer, 29
Bulk genome sequencing, 33
Bulk transcriptome sequencing, 28
Burrow–Wheeler Aligner (BWA), 119
C
Cancer
cause of death, 18
DNA binding domain, 20
genome disease, 18
mutations, 18
research, 18
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3
211