862

Bleidorn, Christophauthor

1st ed. 2017.

1 online resource (XIII, 222 pages 89 illustrations, 87 illustrations in color.)

1. Genomes -- 01.1 Prokaryotes vs. Eukaryotes -- 01.2 Genome Structure -- 01.3 Genome Sizes -- 01.4 Human Genome and Ancient DNA (Neandertaler, Denisova) -- 2. Genomes of Organelles -- 02.1 Mitochondria -- 02.2 Plastids -- 02.3 Outlook Obligate Endosymbionts -- 3. Transcriptomes -- 03.1 mRNA -- 03.2 Transcripts -- 03.3 Expression Level -- 03.4 Alternative Splicing -- 4. Sequencing Techniques -- 04.1 Sanger -- 04.2 Illumina -- 04.3 454 -- 04.4 PacBio -- 04.5 Outlook Nanopore Sequencing -- 5. Genome Sequencing Strategies -- 05.1 Whole Genome Shotgun -- 05.2 RADseq -- 05.3 Target Enrichment -- 05.4 RNAseq -- 6. Assembly and Mapping -- 06.1 Assembling Strategies (kmer vs OLC) -- 06.2 Data Quality and Filtering -- 06.3 Re-Sequencing and Mapping -- 06.4 De novo Assembly Genome -- 06.5 De novo Assembly Transcriptome -- 7. Locating Genes -- 07.1 Orthology vs. Paralogy -- 07.2 BLAST and Successors -- 07.3 Hidden Markov Profile -- 07.4 Ortholog Conjecture -- 8. Alignment -- 08.1 Alignment Strategies -- 08.2 Alignment Masking -- 9. Phylogenetic Analysis -- 09.1 Distance Measurements -- 09.2 Maximum Parsimony -- 09.3 Maximum Likelihood -- 09.4 Bayesian Inference -- 09.5 Supermatrix vs. Single Gene Analysis (Gene Trees vs. Species Trees) -- 10. Systematic Errors in phylogenetic Analysis -- 10.1 Prediction: Evolutionary Models -- 10.2 Heterogenity Nucleotide/Amino Acid-Composition -- 10.3 Variation of substitution rate between the lines -- 10.4 Variation of substitution rate over time -- 10.5 New Approaches to Correct systematic Errors -- 11. Genome-wide Characteristics -- 11.1 Gene Order -- 11.2 Mobile Elements -- 11.3 microRNAs -- 11.4 Differences in the genetic code -- 12. Index -- 13. References.