1 / 12

Group 5 Problem #3 - Annotation of Chlamydia trachomatis Genome

Group 5 Problem #3 - Annotation of Chlamydia trachomatis Genome. Members: Soh Shu E, Peh Bee Keow, Chua Li Ming, Constance, Raquel De Melo Jorge De Magalhaes, Cheong Yuh Meng, Clement, Lee Yie Hou, Zakaria Ali Moh. Almsherqi, Chiang Cern Cher, Samuel.

vic
Download Presentation

Group 5 Problem #3 - Annotation of Chlamydia trachomatis Genome

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Group 5Problem #3 - Annotation of Chlamydia trachomatis Genome Members: Soh Shu E, Peh Bee Keow, Chua Li Ming, Constance, Raquel De Melo Jorge De Magalhaes, Cheong Yuh Meng, Clement, Lee Yie Hou, Zakaria Ali Moh. Almsherqi, Chiang Cern Cher, Samuel

  2. Introduction & Objectives • Introduction – • Chlamydiaare bacterial pathogens andChlamydial trachomatis causes several human diseases of medical significance. • C. trachomatis physiology, structure, developmental biology, and genetics are poorly understood. • The obligate intracellular parasitism of chlamydiae and the lack of any direct or indirect genetic methods for their study has restricted the development of biological and molecular understanding. • Objectives - • Analysis of 1,042,519 bp Chlamydia trachomatis genome to reveal potential features related to the complex, yet poorly understood biology of chlamydiae. • Biocomputational analysis of the chlamydial genome to be done to identify likely protein-coding genes. This was done by similarity searching for functional assignment of known and hypothetical proteins. Sequence similarity clustering of chlamydial genome showed a similar percentage of paralogs with other bacteria of relatively small genomes.

  3. Results • 1,042,519 bp (chromosome) 7493 bp (plasmid) encoding: • 604 (68%) inferred functional proteins. • 35 (4%) similar to hypothetical proteins deposited for other bacteria. • 255 (28%) were not similar to any other sequences. • 32 horizontally transferred genes both from bacterial ancestors and eukaryotic hosts to chlamydiae.

  4. Qn1: Retrieving a paper

  5. Qn2a: How many strains and types of Chlamydia are there? Classification Kingdom: Bacteria Phylum: Chlamydiae Order: Chlamydiales Family: Chlamydiaceae Genus: • Chlamydia • Chlamydophila • Criblamydia • unclassified Chlamydiaceae

  6. Qn2b: Where to obtain the taxonomic tree of Chlamydia trachomatis? Other strains Chlamydia trachomatis (Man) • LGV • MoPn • SFPD • A/SA1/OT (rodent) (pig)

  7. Qn3a: Genome Annotation • Genome Annotation: attaching biological information to sequences • Structural annotation: identification of genomic elements. • Functional annotation: giving biological information to genomic elements. • Gene finding: identifying stretches of sequence that are biologically functional.

  8. Qn3b: Gene Finding – How • Extrinsic Approaches: target genome is Blasted against known sequences. • Ab Initio Approaches: DNA sequence is searched for telltale signs of protein-coding genes. • Prokaryotic genomes: specific and easily identifiable promoter sequences. Glimmer System • Comparative Genomics: DNA sequence is compared to genomes of related species. • Wet Lab to confirm function of a particular gene

  9. http://www.fruitfly.org/GASP1/tutorial/presentation/sld016.htmhttp://www.fruitfly.org/GASP1/tutorial/presentation/sld016.htm

  10. c Plus Strand Gene - Right Arrow c Minus Strand Gene - Left Arrow c Intergenic Region - Both Strands Representative annotated gene segment of plasmid from Chlamydia trachomatis Color Legend Adapted from Gene Image Map Chlamydia trachomatis (http://www.stdgen.lanl.gov/cgi-bin/coordinate.cgi?dbname=chlamy) Qn4a: What is the basis of genome annotation? • To compile and analyse molecular sequence information • For ease of further studies of an organism • For easy location of similar genes or proteins with similar functions located in other organisms.

  11. Qn4b: Bioinformatics tools and techniques that can be used to carry out genome annotation • Artemis - Useful for determining ORFs. • BLASTBasic Local Alignment Search Tool • COGSCluster of Orthologous Groups of Proteins • ProDomprotein domain database • Pfam - for alignment of conserved protein regions. • PDB - for predicting protein 3-D structure. • Psort - for predicting protein localisation in cells. Taken from http://www.stdgen.lanl.gov/cgi-bin/PublicAnnotationHelp.cgi?subdir-stdgen/bacteria#Analytical%20tools

  12. Conclusion • Most of the “eukaryotic” proteins of chlamydia are not related to their animal homologs, Instead, they tend to group with plant proteins in phylogenetic analyses. • Evolution of Chlamydiae as intracellular parasites started with an opportunistic interaction with single-cell amoebal hosts, for a period long enough to acquire the “plant-like” genes, before moving to multicellular invertebrate hosts. • Computational anaylsis helps scientists to elucidate otherwise difficult-to-annotate genomes. By using a wide repertoire of bioinformatics tools, they can help us to draw particular conclusions about species and general ones about evolution

More Related