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Bioinformatics Advance Access originally published online on January 10, 2006
Bioinformatics 2006 22(5):527-531; doi:10.1093/bioinformatics/btk033
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships

Giuseppe D'Auria *, Ravindra Pushker and Francisco Rodriguez-Valera

Evolutionary Genomics Group and Division de Microbiologia, Universidad Miguel Hernandez Campus de San Juan, Apartado 18, 03550 San Juan de Alicante, Spain

*To whom correspondence should be addressed.

Motivation: Lately the use of 16S–23S Intergenic Transcribed Spacer (ITS) sequences for bacterial typing purposes has increased. The presence of conserved regions like tRNA genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare.

Results: A software to study ITSs by a Word Count based System (IWoCS) is proposed. A large dataset of ITS was created (comprising 7355 sequences). A database indicating all the occurrences of possible n-mers (tags), describing each ITS sequence, was created (with n going from 5 to 13) including 32 061 819 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. A dominance plot reflects how common the tags are within different taxonomic levels. The obtained profile identifies highly repeated tags as evolutionarily conserved regions (like tRNA or boxes) or low frequency tags as regions specifically associated to taxonomic groups. The study of the dominance and abundance profiles combined with the taxonomy reports provides a novel tool for the use of the ITS in bacteria typing and identification.

Availability: The database is freely accessible at http://egg.umh.es/iwocs/

Contact: gdauria{at}umh.es

Received on August 19, 2005; revised on December 5, 2005; accepted on December 29, 2005

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