TcSNP: A database of Trypanosoma cruzi genetic variation

ACKERMANN A, CARMONA S, AGÜERO F

Rosario, Santa Fe, Argentina

Congreso; VIII Congreso Argentino de Protozoología y Enfermedades Parasitarias; 2008

Sociedad Argentina de Protozoología

The TcSNP database (http://snps.tcruzi.org) integrates information on genetic variation (polymorphisms, mutations) for different stocks, strains and isolates of Trypanosoma cruzi. The database incorporates sequences (genes from the T. cruzi reference genome, mRNAs, ESTs, and genomic sequences); multiple sequence alignments obtained from these sequences; and single-nucleotide polymorphisms and small indels identified by scanning these multiple sequence alignments. Information in TcSNP can be readily interrogated to arrive at gene sets, or SNP sets of interest based on a number of attributes. For example, the user can ask for all SNPs detected between two particular strains, SNPs that introduce a change in the encoded protein (non-synonymous mutations), SNPs located in genes involved in a particular metabolic pathway, etc. Sequence similarity searches using BLAST are also supported. The first release of Tc-SNP contains nearly 170,000 high confidence candidate SNPs, the majority of which are located in protein coding genes. As new sequence data become available, TcSNP will incorporate these data, mapping new candidate SNPs onto the reference genome sequence. The application, currently under active development, is written in Perl.