Methods and Applications in Comparative Bacterial Genomics

Comparative research of bacterial genomics, now counting in the 100s, produce enormous amounts of information. In an effort to support an organized and successful strategy to genomic analyses, a database driven program with graphic visualization of genomic attributes was made – GenComp. The program was applied to studies of obligate intracellular bacteria. In all of the studies, ORFs were extracted and arranged into ORF-families. Depending on gene order synteny, orthologous clusters of core genes and variable spacer ORFs had been discovered and extracted for alignments and computation of substitution frequencies.The program was applied to the genomes of 6 Chlamydia trachomatis strains to recognize probably the most quickly growing genes. Five genes had been selected for genotyping, and close to a 3-fold higher discrimination capacity was accomplished than that of serotypes.

1 Introduction
1.1 Bacteria
1.1.1 In the service of man
1.1.2 and disservice
1.2 Intracellular lifestyle
1.3 Hunting for genes
1.3.1 The Rickettsiales
1.3.2 Coding DNA
1.3.3 Noncoding DNA
1.3.4 Orphan genes
2 Aims
3 Comparative Bacterial Genomics
3.1 Programming languages
3.1.1 Python
3.1.2 Perl
3.1.3 SQL
3.1.4 Drawbacks of scripting
3.2 Database approach in bioinformatics
3.2.1 Information indexing
3.2.2 Data flows
3.2.3 The relational model
3.2.4 Optimization issues
3.3 Genomic databases
3.3.1 COG DB
3.3.2 ARC DB
3.3.3 GenComp DB
3.4 Sequence alignment
3.5 Gene extraction
3.6 Gene homology clustering
3.7 Positional matching of genes and spacers
3.7.1 Length ratio discrimination of gene clusters
3.7.2 Neighbor-joining of putative orthologs
3.7.3 Reconstruction of ancestral sequences
3.8 Measuring selection using dN/dS
3.9 Phylogenetic methods
3.9.1 Phylogenetic inference
3.9.2 Homology searching in databases
4 The GenComp system
4.1 Background
4.2 Program scripting
4.3 Graphical Viewer
5 Result and Discussion
5.1 Evolution of Rickettsia (I-V)
5.1.1 Rickettsiaceae
5.1.2 GenComp setup
5.1.3 Result and discussion
5.2 Sequence Typing of C. trachomatis (VI)
5.2.1 Chlamydia trachomatis…

Source: Uppsala University Library

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