IWoCS: analyzing ribosomal Intergenic Transcribed Spacer configuration and taxonomic relationships

Abstract

In the last ten years the use of ITS sequences for bacterial typing purposes has increased. The 16S-23S Intergenic Transcribed Spacers (ITS) are characterized by a high variability that allows performing intraspecic discrimination of very close bacterial strains. The presence of conserved regions like tRNA genes or boxes together with hyper variable regions makes the ITS a very complex sequence dificult to analyze and compare. A software to study Intergenic Transcribed Spacers by a Word Count based System (IWoCS) has been proposed. A wide dataset of ITS was created (comprising 6,398 sequences) jointly with a n-mer (with n going from 5 to 10) database where all the occurrences of possible mer, describing each ITS sequence, were collected including 16,509,227 entries. The database allows to analyze ITS sequences submitted by users using a web based interface. The abundance in the database of each n-mer is given in a one-base sliding frame. The obtained profile identifies common n-mers as conserved regions (like tRNA or boxes) or rare n-mers as unique regions with corresponding taxonomic specificity. The study of the obtained profile highlights conserved or strain specific regions with a concomitant taxonomy report. Each mer could be used to retrieve the corresponding sequences for subsequent taxonomy or relationship analysis.

Citation

D'Auria G., Pushker R. and Rodríguez-Valera F. (2006) IWoCS: analyzing ribosomal Intergenic Transcribed Spacer configuration and taxonomic relationships. Bioinformatics, 22(5):527-531.