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Computational evaluation of TIS annotation for prokaryotic genomes

Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu, Zhen-Su She
2008 BMC Bioinformatics  
of the reliability of TIS annotations for any prokaryotic genome.  ...  Conclusion: Large-scale computational evaluation of TIS annotation has been achieved.  ...  Acknowledgements We thank Yongchu Liu, Xiaojing Yang, Yifan Yang and Xinqiu Yao for beneficial discussions.  ... 
doi:10.1186/1471-2105-9-160 pmid:18366730 pmcid:PMC2362131 fatcat:v24alvvjtnebpfw4em24y3mudi

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

G.-Q. Hu, X. Zheng, Y.-F. Yang, P. Ortet, Z.-S. She, H. Zhu
2007 Nucleic Acids Research  
Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation  ...  Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved  ...  ACKNOWLEDGEMENTS Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm799 pmid:17942412 pmcid:PMC2238952 fatcat:kzxhdygoq5c4zod2edbx2r4j4a

An unsupervised classification scheme for improving predictions of prokaryotic TIS

Maike Tech, Peter Meinicke
2006 BMC Bioinformatics  
Recently a number of post-processing tools have been proposed for improving the annotation of prokaryotic TIS.  ...  Therefore prior assumptions about the properties of prokaryotic gene starts may cause suboptimal predictions for newly sequenced genomes with TIS signals differing from those of well-investigated genomes  ...  We thank Nico Pfeifer for implementing parts of the TICO web server and Burkhard Morgenstern for proof-reading of the manuscript.  ... 
doi:10.1186/1471-2105-7-121 pmid:16526950 pmcid:PMC1434772 fatcat:a7mpxu6kcffmpegxsed5w6yylm

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, Zhen-Su She
2007 BMC Bioinformatics  
Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies.  ...  Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of  ...  O'Brien for kindly reading and revising the manuscript. We also thank Prof. Chun-Ting Zhang for providing ZCURVE 1.0 program.  ... 
doi:10.1186/1471-2105-8-97 pmid:17367537 pmcid:PMC1847833 fatcat:pi334snxdvag5gazp5efll775e

Where Are The Genes Missing From Prokaryotic Genomes?

Luciano Brocchieri
2015 Journal of Phylogenetics & Evolutionary Biology  
] or NPACT [3], may have a greater impact on the amelioration of genome annotations than any remaining improvement in sensitivity of computational prokaryotic-gene-prediction methods.  ...  conserved in sequence and in length across bacterial genera or phyla, thus "discovering" in these genomes many "new" genes, and providing a useful tool for the amelioration of prokaryotic genome annotations  ...  ] or NPACT [3] , may have a greater impact on the amelioration of genome annotations than any remaining improvement in sensitivity of computational prokaryotic-gene-prediction methods. .  ... 
doi:10.4172/2329-9002.1000e114 fatcat:w7sy4pnvpjh4nizmilpy6evyve

smORFer: a modular algorithm to detect small ORFs in prokaryotes [article]

Alexander Bartholomäus, Baban Kolte, Ayten Mustafayeva, Ingrid Goebel, Stephan Fuchs, Susanne Engelmann, Zoya Ignatova
2020 bioRxiv   pre-print
Yet, they have difficulties evaluating prokaryotic genomes due to the unique architecture of prokaryotic genomes (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation  ...  Yet, the identification of functional small proteins and the systematic genome annotation of their cognate small open reading frames (smORFs) remains challenging both experimentally and computationally  ...  These approaches have difficulties evaluating prokaryotic genomes due to their unique architecture, including polycistronic messages, large fraction of overlapping ORFs, leaderless translation and lack  ... 
doi:10.1101/2020.05.21.109181 fatcat:jrsqstv6qndvfbi5rk5c63mrma

Gene prediction in metagenomic fragments: A large scale machine learning approach

Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke
2008 BMC Bioinformatics  
available methods for genomes of single species.  ...  The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy.  ...  Heiko Liesegang for supporting the development of our method. We are grateful to Andrew Woehler for proofreading the final version of our manuscript.  ... 
doi:10.1186/1471-2105-9-217 pmid:18442389 pmcid:PMC2409338 fatcat:f63d4jpihndutayeoqpyui5o6e

Balrog: A universal protein model for prokaryotic gene prediction

Markus J. Sommer, Steven L. Salzberg, Christos A. Ouzounis
2021 PLoS Computational Biology  
We have developed a universal model of prokaryotic genes by fitting a temporal convolutional network to amino-acid sequences from a large, diverse set of microbial genomes.  ...  Automatic genome annotation tools are integral to understanding these organisms, yet older gene finding methods must be retrained on each new genome.  ...  Center for Computational Biology Slack channel for voting on said cool names, Martin Steinegger for helpful conversations and creating MMseqs2, @genexa_ch for providing via Twitter a small set of diverse  ... 
doi:10.1371/journal.pcbi.1008727 pmid:33635857 fatcat:j5wb3hbsn5gxhnbvbphzyfwuty

Accuracy improvement for identifying translation initiation sites in microbial genomes

H.-Q. Zhu, G.-Q. Hu, Z.-Q. Ouyang, J. Wang, Z.-S. She
2004 Bioinformatics  
These results show that * To whom correspondence should be addressed. our algorithm is one of the most accurate methods to identify TIS of prokaryotic genomes.  ...  Motivation: At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3 end), but a much lower accuracy of  ...  -T.Zhang at Tianjin University (China) for providing GS-Finder program and part of datasets.  ... 
doi:10.1093/bioinformatics/bth390 pmid:15247104 fatcat:dc22pvbqgrebzcbpqbfnb3jrte

smORFer: a modular algorithm to detect small ORFs in prokaryotes

Alexander Bartholomäus, Baban Kolte, Ayten Mustafayeva, Ingrid Goebel, Stephan Fuchs, Dirk Benndorf, Susanne Engelmann, Zoya Ignatova
2021 Nucleic Acids Research  
They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.).  ...  Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally.  ...  These approaches have difficulties evaluating prokaryotic genomes due to their unique architecture, including polycistronic messages, large fraction of overlapping ORFs, leaderless translation and lack  ... 
doi:10.1093/nar/gkab477 pmid:34125903 fatcat:cotv62o2y5fejaaldplcy6x7o4

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

Elvis Ndah, Veronique Jonckheere, Adam Giess, Eivind Valen, Gerben Menschaert, Petra Van Damme
2017 Nucleic Acids Research  
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes.  ...  REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs.  ...  As curation-based methods cannot keep pace with the increase in the number of available bacterial genomes, researchers have reverted to the use of computational methods for prokaryotic genome annotation  ... 
doi:10.1093/nar/gkx758 pmid:28977509 pmcid:PMC5714196 fatcat:pdbsojhhqnho7nwt6ujcf7o2iq

The loose evolutionary relationships between transcription factors and other gene products across prokaryotes

Marc del Grande, Gabriel Moreno-Hagelsieb
2014 BMC Research Notes  
We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available.  ...  We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome.  ...  Since predicted TFs produced similar results to those obtained with manually-annotated TFs, we concluded that genes coding for predicted TFs in other prokaryotes would yield appropriate results to evaluate  ... 
doi:10.1186/1756-0500-7-928 pmid:25515977 pmcid:PMC4300776 fatcat:uccl3xatljc5xclrrxk3cck4ie

Benchmarking of Methods for Genomic Taxonomy

M. V. Larsen, S. Cosentino, O. Lukjancenko, D. Saputra, S. Rasmussen, H. Hasman, T. Sicheritz-Ponten, F. M. Aarestrup, D. W. Ussery, O. Lund
2014 Journal of Clinical Microbiology  
In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based  ...  The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases.  ...  We are grateful to Keith Jolley, Department of Zoology, University of Oxford, United Kingdom, for providing us with the rMLST genes for the genomes of the training data.  ... 
doi:10.1128/jcm.02981-13 pmid:24574292 pmcid:PMC3993634 fatcat:ng375ay2ozarnlsuxrlvofxfai

Improving pan-genome annotation using whole genome multiple alignment

Samuel V Angiuoli, Julie C Dunning Hotopp, Steven L Salzberg, Hervé Tettelin
2011 BMC Bioinformatics  
Results: We introduce a new tool, Mugsy-Annotator, that identifies orthologs and evaluates annotation quality in prokaryotic genomes using whole genome multiple alignment.  ...  An evaluation of species pan-genomes using the tool indicates that such anomalies are common, especially at translation initiation sites.  ...  We thank David Riley and Sean Daugherty for valuable discussions and feedback.  ... 
doi:10.1186/1471-2105-12-272 pmid:21718539 pmcid:PMC3142524 fatcat:lcszsxtmkzfgxing5arwprsiiy

Bacterial riboproteogenomics: the era of N-terminal proteoform existence revealed

Daria Fijalkowska, Igor Fijalkowski, Patrick Willems, Petra Van Damme
2020 FEMS Microbiology Reviews  
With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity.  ...  Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are incomplete, even for so-called well-annotated genomes.  ...  This complexity remains poorly captured in current prokaryotic genome annotations.  ... 
doi:10.1093/femsre/fuaa013 pmid:32386204 fatcat:7njiboek7rasho26indgx2bkn4
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