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  1. Interrupted coding sequences DB
    Full Name of the Resource : Interrupted coding sequences: frameshifts, stop codons, sequencing errors in microbial genomes
    Resource Category : Databases -> Genomic Databases (Non-Human) -> Prokaryotic Genome Databases - General

    Brief Description : Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) that can seriously affect all subsequent steps of functional characterisation, 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 localisation with the surrounding sequence. Furthermore, to facilitate the experimental characterisation of ICDS, we propose optimised 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, 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.
    Subject Area : Microbial Genomics


    Institute/s :
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch Cedex, France
    Address of Institute/s :
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France
    Country : France


    Authors/Contributors : Odile Lecompte; Emmanuel Perrodou; Caroline Deshayes; Jean Muller; Christine Schaeffer; Alain Van Dorsselaer; Raymond Ripp; Olivier Poch; Jean-Marc Reyrat
    Contact Email : lecompte@igbmc.u-strasbg.fr
    Year : 2005