Thursday, December 29, 2005

IWoCS is accepted

There can't be anything better to end this year. Today one research article IWoCS has been accpeted for publication in Bioinformatics.


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.