Blom, Jochen: Comparative genomics on gene and single nucleotide level. 2013
Inhalt
- Introduction
- Comparative genome analyses in times of ultrafast sequencing
- First generation sequencing: Sanger sequencing
- Second generation sequencing
- Assembly: From reads to complete genomes
- From contigs to scaffolds: Paired-end sequencing
- Draft genomes vs. finished genomes
- Tools for contig layout and genome finishing
- Comparative genomics
- Historical background
- Terminology
- Genomic subsets
- The bacterial pan genome
- Applications in medical, industrial, and fundamental research fields
- Parallelization in Biosequence Analysis
- Motivation and goals of this work
- Comparative genomics on gene level: EDGAR
- Previous approaches
- VISTA tools
- CMR - Comprehensive Microbial Resource
- MBGD - MicroBial Genomes Database
- Sybil
- Panseq
- CoGE
- SEED
- STRING
- EDGAR: Efficient Database framework for comparative Genome Analysis using BLAST score Ratios
- Comparative genomics on single nucleotide level: SARUMAN
- Short read alignment in modern sequence analysis
- Previous approaches
- SARUMAN: Semiglobal Alignment of short Reads Using CUDA and NeedleMAN-Wunsch
- Discussion
- Appendix