Molecular and bioinformatics methods for direct sequencing

摘要

A method for preparing and isolating nucleic acids from a sample comprising: contacting the sample with a chaotropic agent and subjecting the sample to lysis; and optionally, contacting the sample with activated charcoal either before, during or after the lysis step. Additional purification steps involve guanidine salts, isopropanol, detergents and mechanical lysis. Ideally the resultant DNA or RNA sample may be stored at an ambient (room?) temperature for several weeks. Ideally the sample comprises 16S ribosomal RNA. Also disclosed are the preparation of an isolated biological sample containing at least one DNA or RNA using a chaotropic agent and silicon dioxide, methods for separating SSU rRNA and reverse transcribing it, a method of sequencing and sequencing data classification by data analysis, a computer implemented method of sequencing data analysis. Various permutations of the extraction, sequencing and data analysis methods are also disclosed.