Desenvolvimento de ferramentas computacionais para análise T-RFLP in silico do gene ribossômico 16S

Abstract

Techniques for genetic fingerprinting and independent cultivation approaches have been used extensively to evaluate the diversity of microbial communities in various environments. However, determining the composition of species present in these communities is not an easy task, typically requiring expensive and laborious testing. In this context, T-RFLP (terminal restriction fragment length polymorphism), used to determine the structure of complex microbial communities for examining polymorphisms of DNA restriction fragments, is a practical, robust and reliable tool. The prediction taxonomy of terminal restriction fragments (T-RFs) can be achieved using the 16S rDNA sequence of bacteria present on the World Wide Web (www). Thus, it developed a set of computational tools, called OneSix, for T-RFLP analysis in silico of sequences present in public domain databases. Therefore, such sequences was conducted by PCR amplification (Polymerase Chain Reaction) and in silico digestion of the 16S rDNA sequences cured, present in the site SILVA, using the sequences of 11 forward primers, reverse primers 10 and 13 enzymes restriction, commonly used in T-RFLP technique. The algorithms were developed in the Ruby programming language, due to a broad class of packets directed to methods and bioinformatics, the bioruby; and tested by simulating the PCR, resulting in 81 files and T-RFLP, in 1053 files. The OneSix intends to facilitate the prediction process Taxonomic T-RFs by researchers in the field, by generating comprehensive and relevant data to the reality of T-RFLP technique. Keywords: Computational tool. T-RFLP. 16S rDNA. Ruby language.