MiCA: web-based computational tools for the analysis of microbial community structure and composition based on T-RFLP of 16S rRNA genes

Analyses of microbial community structure based on terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes are hindered by the lack of computational tools needed to aid experimental design, and to archive and analyze large data sets. The aim of this research was to develop a suite of Web-based tools that would enable researchers to perform several tasks, including: (a) in silico PCR amplification and restriction of 16S rRNA gene sequences found in public databases; (b) automatic retrieval of data and archival storage in an Oracle relational database; (c) comparison of multiple T-RFLP profiles obtained from a single sample using different primer-enzyme combinations; and (d) statistical analysis of T-RFLP data and clustering of samples based on similarities and differences.