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website tour - tcsnp


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website tour - tcsnp

  1. 1. TcSNP –  A map of Trypanosoma cruzi genetic variation WebSite Tour Laboratorio de Genómica y Bioinformática Instituto de Investigaciones Biotecnológicas Universidad de San Martín
  2. 2. What is TcSNP? TcSNP  is  an  online  resource  with  information  on  genetic  variation  (polymorphisms,  mutations)  for  different  stocks,  strains  and  isolates  of  Trypanosoma  cruzi, the causative agent of Chagas Disease June, 2008 2
  3. 3. What can you do in TcSNP? ●Access a sequence alignment containing your gene of interest, see  polymorphic sites, type of mutation, dN/dS ratio, etc. ●Find aligned genes/sequences that satisfy specific rules: participate in a given  metabolic pathway, has more/less than a given number of SNPs,  has a  particular dN/dS ratio, etc. ●Find SNPs based on diferent criteria: detected between specific strains, that  cause synonymous/non­synonymous/non­sense mutations,etc. ●Combine single queries making complex queries (doing unions, intersetions,  and substractions of queries) ●Explore multiple sequence alignments June, 2008 3
  4. 4. home page Search by  genes and alignment criteria Examine and combine your Search by  queries SNPs criteria Search by  sequence similarity (BLAST) June, 2008 4
  5. 5. search for genes June, 2008 5
  6. 6. retrieved list of genes Let's see the alignment June, 2008 6
  7. 7. alignment view: general information June, 2008 7
  8. 8. alignment view: overview June, 2008 8
  9. 9. alignment view: aligned sequences with SNPs June, 2008 9
  10. 10. search for SNPs Example SNP Query #1: Find polymorphic sites between two strains  June, 2008 10
  11. 11. retrieved list of SNPs Let's see more  information on  this SNP June, 2008 11
  12. 12. SNP view: general information Let's see this SNP in its  alignment June, 2008 12
  13. 13. SNP in alignment­context June, 2008 13
  14. 14. search for SNPs Example SNP Query #2: Select high­score SNPs June, 2008 14
  15. 15. combine queries June, 2008 15
  16. 16. combine queries Query #3: high­score SNPs detected  between strains CL Brener and Tul2 June, 2008 16
  17. 17. Thanks! June, 2008 17