MLST (multi-locus sequence typing)
Desarrollo propio de Pipeline para genotipificar usando el esquema MLST.Actualmente está disponible solicitando acceso via e-mail a: email@example.com
Multilocus sequence typing (MLST) is an unambiguous procedure for characterizing isolates of microorganism species using the sequences of internal fragments of seven house-keeping genes. Approx. 450-500 bp internal fragments of each gene are used, as these can be accurately sequenced on both strands using an automated DNA sequencer. For each house-keeping gene, the different sequences present within a microorganism species are assigned as distinct alleles and, for each isolate, the alleles at each of the seven loci define the allelic profile or sequence type (ST). MLST has been successfully used to study population genetics and to reconstruct micro-evolution of epidemic bacteria, fungus and protozoa. Highly reproducible data together with the availability of low-cost sequencing services make MLST a powerful tool. However, manually intensive steps of processingraw sequence data files and downstream analysis hindered the application of the methodology. In the lastyears, several bioinformatic workflow systems have emerged due to big data. Among them Galaxy, an open web-based platform for data intensive processing (http://galaxyproject.org/), is a powerful and flexible alternative for the analysis genomics and postgenomics projects. Here, we introduce MLST-pipeline, a Galaxy-base tool for dealing with Multi Locus Sequence Typing data analysis. Dedicated tools for data uploading (raw chromatogram or fasta files), base calling (PHRED), contig assembling(CAP3), sequence trimming.
Sergio Gonzalez, Silvina Wilkowsky, Eliana Guillemi, Sofia de la Fourniere, Mariano Fernandez Miyakawa, Leandro Redondo, Juan Diaz Carrazco.
Adherido al SNDG desde 30-06-2016
Centro de Investigación en Ciencias Veterinarias y Agronómicas (107)