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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

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Annotation of Sarcocystis neurona scaffolds

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  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!!! 

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