*Biovar - A strain differentiated from other strains by biochemical or other non-serological means.

:Abedon, S. T. (1998) Supplemental Lecture (98/04/14 update). <http://www.mansfield.ohio-state.edu/~sabedon/biol3010.htm>. Accessed 10 November 2013.

*Clusters of orthologous groups (COGs) - A group of at least three proteins that have the same evolutionary origin.

:Koonin, E.V. (2013) The Clusters of Orthologous Groups (COGs) Database: Phylogenetic Classification of Proteins. from Complete Genomes. In J. McEntyre & J. Ostell (Eds). ''The NCBI Handbook''. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK21090/. Accessed 11 November 2013.

*Contig - Copies of pieces of DNA that represent the overlapping regions of a chromosome.

:U.S. Department of Energy Human Genome Project (2013) The Human Genome Project Information Archive 1990-2003. <http://web.ornl.gov/sci/techresources/Human_Genome/glossary.shtml>. Accessed 10 November 2013.

*Hydrodynamic shearing - A technique that fragments DNA molecules by forcing them through a small orifice or the bore of a small-diameter tube at high velocity.

:Joneja, A. & Huang, X. (2009) Supplementary Material For: A device for automated hydrodynamic shearing of genomic DNA. ''BioTechniques'' '''46''': 553–556.

*Paralog - Genes that are homologous and are a result of gene duplication.

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==Outline of the Article==

===Methods used to annotate the genome===

*The programs PEPDATA and FRAMES were used to translate the chlamydial genome.

*BLASTP was used to find open reading frames in the ''C. trachomatis'' genome.

*RNAse P RNA, tRNAs, and rRNAs were identified using BLASTN.

*BLASTP-(-mp4-option) and CLUSTALW were used to estimate the location of start codons by looking for conserved sequences.

*GeneMark and Glimmer were used to evaluate the predicted start codons.

*When more than one start codon was identified for a given protein sequence, the first of the codons to appear in the genome was set as the start codon.

*PSI-BLAST was used to detect homologs to chlamydial protein sequences.

*EMOTIF was used to analyze sequence motifs.

*The COGNITOR program was used to compare chlamydial protein sequences to Clusters of Orthologous Groups.

*The above analysis resulted in the identification of 894 protein-coding genes and functional assignment for 604 of these genes.

*35 chlamydial protein-coding genes were found to be similar to known genes in other bacteria.

*There are 256 chlamydial proteins that are paralogs belong to 58 families of similar genes.

===Analysis of gene expression pathways===

*Within the inclusion, ''C. trachomatis'' present today likely do not exchange genetic information with the host often because there are no genes in the chlamydial genome that are homologous to genes that are transposons or are involved in transformation or the acquirement of foreign DNA.

*Despite the aforementioned, Table 1 in the paper provides evidence that a majority of the genes in ''C. trachomatis'' are a result of horizontal gene transfer with bacterial ancestors or eukaryotic hosts.

*Figure 3 traces the origins of the chlamydial enoyl-acyl carrier protein reductase through various organisms supporting the theory that some chlamydial genes originated from horizontal gene transfer with eukaryotes.

*The mechanisms of chromatin condensation-decondensation may be related to that in eukaryotes as evidenced by the discovery of SET and SWIB domains in the chlamydial genome previously only found in eukaryotes.

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