ArticleNucleic acids research2006
ICDS database: interrupted CoDing sequences in prokaryotic genomes.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 21 citations in OpenAlex.
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- Re-annotation of protein-coding genes in 10 complete genomes of Neisseriaceae family by combining similarity-based and composition-based methods.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- Conservation and revised annotation of the Treponema denticola prcB-prcA-prtP locus encoding the dentilisin (CTLP) protease complex.Molecular oral microbiology · 2013Article
- Translational recoding in archaea.Extremophiles : life under extreme conditions · 2012Review
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- High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.BMC genomics · 2008Article
- Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions.BMC genomics · 2008Article
- Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences.BMC evolutionary biology · 2008Article
- Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton.BMC genomics · 2007Article
- Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.BMC bioinformatics · 2007Article
- Gene decay in archaea.Archaea (Vancouver, B.C.) · 2007Article
- Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition.Genome biology · 2007Article
- Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?Genome biology · 2007Article
- The gene of an archaeal alpha-L-fucosidase is expressed by translational frameshifting.Nucleic acids research · 2006Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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