1 / 20

Annotation of Sarcocystis neurona scaffolds

Annotation of Sarcocystis neurona scaffolds . Nigel Austin Turgay Ibrikci Liliana Lopez Kleine Marton Megyeri. Caribbean Training Programme on Bioinformatics January 2010. Sarcocystis neurona. Genus: Sarcocystis - parasitic protozoa

cheri
Télécharger la présentation

Annotation of Sarcocystis neurona scaffolds

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. Annotation of Sarcocystisneurona scaffolds Nigel Austin TurgayIbrikci Liliana Lopez Kleine MartonMegyeri Caribbean Training Programme on Bioinformatics January 2010

  2. Sarcocystisneurona • Genus: Sarcocystis - parasitic protozoa • occur as sporocysts in the muscle of mammals, birds, and reptiles. • In humans – asymptomatic • Sarcocystisneuronacauses equine protozoalmyoencephalitis

  3. S. neurona& Related Apicomplexa Eimeria Sarcocystisneurona Neospora Toxoplasma

  4. Life Cycle of S. neurona

  5. About Data • Data cordially supplied by Dr. Jessica Kissinger who very recently acquired the genome sequence • First 120,000 bp in 4 scaffolds – analysis • Then 400,000 bp in 4 scaffolds - analysis

  6. Objectives • To annotate novel DNA sequences of S. neurona. • Detection of coding sequences by: • comparison with other sequences in data bases • NB: No reference genome or other info was available since sequences were novel

  7. Strategy for Scaffolds • BLASTX in nr db: searchof translated sequence in protein databases • TBLASTX in est db: search of translated sequence in translated sequence databases • Comparison in ACT with most closely related organisms (Toxoplasmagondii and Neosporacaninum)

  8. Results – Blast Search

  9. Results BLAST

  10. ACT Results Match of region with a conserved gene in Neosporacaninumand Toxoplasmagondii Neosporacaninum scaffolds

  11. Hmmm…. • No genes in 400,000 bp DNA??? • And then…. • Expertise, experience • He was able to locate a gene

  12. Gene Discovered! Match of region with a conserved gene in Neosporacaninum

  13. Discovered Gene - Gene1 • The discovered gene was expanded on both the 5’ and 3’ end • Start and stop codons were identified • Protein sequence was determined • BLAST – hypothetical protein with high similarity to one found in NeosporaandToxoplasma

  14. Gene Comparison Match of region with a conserved gene in Neosporacaninumand Toxoplasmagondii Neighbouring genes are not present in the scaffold.

  15. Results – UniprotSearch Performed with GENE1

  16. Further Protein Info • Characterize our protein product • Membrane protein? High regions of hydrophobicity • Domains and motifs • Secondary structures

  17. Hydrophobicity Graph No transmembrane motifs present

  18. Domains & Motifs

  19. Conclusion • Various blast searches may assist in location of orthologous genes in other genomes • ACT very useful tool for gene discovery and annotation (along with experience & expertise) • One gene (Gene1) was found in 400 Kb of DNA – scaffolds perhaps in a gene poor region of genome • Gene1 is perhaps orthologous with a gene in Toxoplasma and Neurospora • Hypothetical gene – no function prescribed to it

  20. Thank You!!! 

More Related