Perrodou_2006_Nucleic.Acids.Res_34_D338

Unrecognized frameshifts in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence ICDS that can seriously affect all subsequent steps of functional characterization from in silico analysis to high-throughput proteomic projects Here we describe the Interrupted CoDing Sequence database containing ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes ICDS can be retrieved by species browsing or similarity searches via a web interface http:\/\/www-bio3d-igbmc.u-strasbg.fr/ICDS The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence Furthermore to facilitate the experimental characterization of ICDS we propose optimized primers for re-sequencing purposes The database will be regularly updated with additional data from ongoing sequenced genomes Our strategy has been validated by three independent tests i ICDS prediction on a benchmark of artificially created frameshifts ii comparison of predicted ICDS and results obtained from the comparison of the two genomic sequences of Bacillus licheniformis strain ATCC 14580 and iii re-sequencing of 25 predicted ICDS of the recently sequenced genome of Mycobacterium smegmatis This allows us to estimate the specificity and sensitivity 95 and 82 respectively of our program and the efficiency of primer determination.