ArticleNucleic acids research1998
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.
Article in Nucleic acids research, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 181 citations in OpenAlex.
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- Gene Prediction in Metagenomic Fragments with Deep Learning.BioMed research international · 2017Article
- A Primer on Infectious Disease Bacterial Genomics.Clinical microbiology reviews · 2016Review
- Complete Genome Sequence of Xanthomonas campestris pv. campestris Strain 17 from Taiwan.Genome announcements · 2015Article
- SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes.Journal of bacteriology · 2014Article
- Jaccard index based similarity measure to compare transcription factor binding site models.Algorithms for molecular biology : AMB · 2013Article
- How many signal peptides are there in bacteria?Environmental microbiology · 2013Article
- The automatic annotation of bacterial genomes.Briefings in bioinformatics · 2013Article
- A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus.The ISME journal · 2013Article
- Gene prediction in metagenomic fragments based on the SVM algorithm.BMC bioinformatics · 2013Article
- The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain.BMC genomics · 2012Article
- DNA-energetics-based analyses suggest additional genes in prokaryotes.Journal of biosciences · 2012Article
- Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome.BMC microbiology · 2011Article
- Identification of prokaryotic small proteins using a comparative genomic approach.Bioinformatics (Oxford, England) · 2011Article
- Article
- A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.Genome biology and evolution · 2011Article
- A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.Journal of bacteriology · 2010Article
- Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning.BMC genomics · 2010Article
- Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen.BMC genomics · 2010Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of a newly sequenced bacterial genome starts with identification of protein-coding genes. Functional assignment of proteins requires the exact knowledge of protein N-termini. We present a new program ORPHEUS that identifies candidate genes and accurately predicts gene starts. The analysis starts with a database similarity search and identification of reliable gene fragments. The latter are used to derive statistical characteristics of protein-coding regions and ribosome-binding sites and to predict the complete set of genes in the analyzed genome. In a test on Bacillus subtilis and Escherichia coli genomes, the program correctly identified 93.3% (resp. 96.3%) of experimentally annotated genes longer than 100 codons described in the PIR-International database, and for these genes 96.3% (83.9%) of starts were predicted exactly. Furthermore, 98.9% (99.1%) of genes longer than 100 codons annotated in GenBank were found, and 92.9% (75.7%) of predicted starts coincided with the feature table description. Finally, for the complete gene complements of B.subtilis and E.coli , including genes shorter than 100 codons, gene prediction accuracy was 88.9 and 87.1%, respectively, with 94.2 and 76.7% starts coinciding with the existing annotation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.