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Laboratorio de Genómica y BioinformáticaLaboratorio de Genómica y BioinformáticaInstituto de Investigaciones Biotecnológicas
Universidad de San Martín
TcSNP – A map of Trypanosoma cruzi genetic variation
June, 2008 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 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
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home page
http://snps.tcruzi.org
Search by genes andalignmentcriteria
Search by SNPs criteria
Examine andcombine yourqueries
Search by sequencesimilarity(BLAST)
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search for genes
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retrieved list of genes
Let's see the alignment
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alignment view: general information
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alignment view: overview
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alignment view: aligned sequences with SNPs
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search for SNPs
Example SNP Query #1: Find polymorphic sites between two strains
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retrieved list of SNPs
Let's see more information on this SNP
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SNP view: general information
Let's see this SNP in its alignment
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SNP in alignmentcontext
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Example SNP Query #2: Select highscore SNPs
search for SNPs
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combine queries
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combine queries
Query #3: highscore SNPs detected between strains CL Brener and Tul2
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Thanks!
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