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HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes

S. Garcia-Vallve
2003 Nucleic Acids Research  
The Horizontal Gene Transfer DataBase (HGT-DB) is a genomic database that includes statistical parameters such as GþC content, codon and amino-acid usage, as well as information about which genes deviate  ...  in these parameters for prokaryotic complete genomes.  ...  ACKNOWLEDGEMENTS We thank Kevin Costello of the Language Service of the Rovira i Virgili University for his help with writing the manuscript, and TINET for hosting the database.  ... 
doi:10.1093/nar/gkg004 pmid:12519978 pmcid:PMC165451 fatcat:mwpew5uoujhe5pe7vq3jf7z2xi

OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes

L.-W. Jiang, K.-L. Lin, C. L. Lu
2008 Nucleic Acids Research  
OGtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes.  ...  It then downloads their complete genomes from the National Centre for Biotechnology Information and identifies OGs in each genome and their orthologous OGs in other genomes.  ...  ACKNOWLEDGEMENTS This work was supported in part by National Science Council of Republic of China under grant NSC96-2221-E-009-126 and in part by the ATU plan of MOE.  ... 
doi:10.1093/nar/gkn240 pmid:18456706 pmcid:PMC2447762 fatcat:raix25nbazgldefxdamna4fdxe

Displacement of ɛ-proteobacterial core genes by horizontally transferred homologous genes

Tom Coenye, Peter Vandamme
2005 Research in Microbiology  
The introduction of novel genes by horizontal gene transfer (HGT) is considered an alternative mechanism for genetic adaptation, leading to diversification and speciation.  ...  Among the 991 core genes found in all five completed ε-proteobacterial genome sequences, we identified 30 genes that were probably acquired by HGT.  ...  Acknowledgements T.C. and P.V. are indebted to the Fund for Scientific Research, Flanders (Belgium) for a position as postdoctoral fellow and research grants, respectively.  ... 
doi:10.1016/j.resmic.2005.01.016 pmid:15950129 fatcat:gqxhuctyenhwzfuzaqwi5ppg2m

Causes of Insertion Sequences Abundance in Prokaryotic Genomes

Marie Touchon, Eduardo P. C. Rocha
2007 Molecular biology and evolution  
Gene transfer is also not a significant determinant of the abundance of IS elements in genomes, suggesting that IS abundance is controlled at the level of transposition and ensuing natural selection and  ...  The current availability of hundreds of genomes renders testable many of these hypotheses, notably that IS abundance correlates positively with the frequency of horizontal gene transfer (HGT), genome size  ...  Acknowledgments We thank Guillaume Achaz, Isabelle Gonc xalves, and the reviewers for comments and criticisms on previous versions of this manuscript.  ... 
doi:10.1093/molbev/msm014 pmid:17251179 fatcat:bwibbfxwjba2xoq3bckml2gwrq

An acquisition account of genomic islands based on genome signature comparisons

M W J van Passel, A Bart, H H Thygesen, A C M Luyf, A H C van Kampen, A van der Ende
2005 BMC Genomics  
Recent analyses of prokaryotic genome sequences have demonstrated the important force horizontal gene transfer constitutes in genome evolution.  ...  We assessed the compositional similarity and putative acquisition account of these GIs using the genome signature. For this analysis we developed a new algorithm, available as a web application.  ...  Acknowledgements We would like to thank the two anonymous reviewers of this paper for their helpful suggestions.  ... 
doi:10.1186/1471-2164-6-163 pmid:16297239 pmcid:PMC1310630 fatcat:6q7a4g3v5fh7no6nbqy4g2roce

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

Georgios S. Vernikos, Julian Parkhill
2006 Computer applications in the biosciences : CABIOS  
Motivation: There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods.  ...  We applied the IVOM approach to the genome of Salmonella enterica serovar Typhi CT18, a well-studied prokaryote in terms of HGT events, and we show that the IVOMs outperform state-of-the-art low and high  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btl369 pmid:16837528 fatcat:xfa5figccjgpvaya2ldexsezey

Phylogenomic Evidence for a Myxococcal Contribution to the Mitochondrial Fatty Acid Beta-Oxidation

Agatha Schlüter, Iñaki Ruiz-Trillo, Aurora Pujol, Jonathan H. Badger
2011 PLoS ONE  
We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes.  ...  Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown.  ...  Parts of the simulations were performed using the freely available CIPRES-Portal 1.0 and 2.0 [46] and Bioportal (www.bioportal.uio.no) [51] .  ... 
doi:10.1371/journal.pone.0021989 pmid:21760940 pmcid:PMC3131387 fatcat:slha4p2nonebpkg3pb57ewbr4y

Reconstructing genome trees of prokaryotes using overlapping genes

Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu, Chin Lung Lu
2010 BMC Bioinformatics  
trees of prokaryotes according to their overlapping genes.  ...  as a pair of overlapping genes.  ...  Acknowledgements This work was supported in part by National Science Council of Republic of China under grant NSC97-2221-E-009-081-MY3.  ... 
doi:10.1186/1471-2105-11-102 pmid:20181237 pmcid:PMC2845580 fatcat:nidfl4davrhdfl2v6xxsueie2y

GISMO--gene identification using a support vector machine for ORF classification

L. Krause, A. C. McHardy, T. W. Nattkemper, A. Puhler, J. Stoye, F. Meyer
2006 Nucleic Acids Research  
We found that it performs well for complete prokaryotic chromosomes, irrespective of their GC content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition  ...  We present the novel prokaryotic gene finder GISMO, which combines searches for protein family domains with composition-based classification based on a support vector machine.  ...  The authors also thank Santi Garcia-Vallve for supplying information for the genomes contained in HGT-DB. L.K. was supported by the DFG Graduiertenkolleg 635 Bioinformatik.  ... 
doi:10.1093/nar/gkl1083 pmid:17175534 pmcid:PMC1802617 fatcat:j33nuxiigngjbfmzw25gcwqo6i

Web-based graphical querying of databases through an ontology

Diego Calvanese, C. Maria Keet, Werner Nutt, Mariano Rodríguez-Muro, Giorgio Stefanoni
2010 Proceedings of the 2010 ACM Symposium on Applied Computing - SAC '10  
We have evaluated our system for Web-ONtology baseD Extraction of Relational data (WONDER) with an existing large genomics database about horizontal gene transfer and found that it meets both the scalability  ...  To satisfy further information needs, users currently have to have a good understanding of SQL and how the data is stored in the database.  ...  We have evaluated this infrastructure with the horizontal gene transfer genomics database HGT-DB.  ... 
doi:10.1145/1774088.1774384 dblp:conf/sac/CalvaneseKNRS10 fatcat:7a65hh3hwfa7ljh23lme45pvz4

Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers

J. Grilli, M. Romano, F. Bassetti, M. Cosentino Lagomarsino
2014 Nucleic Acids Research  
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. ABSTRACT Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss.  ...  of members of the family found on a given genome).  ...  The first data set, HGT-DB (24), scores putative horizontal transfers on a set of 959 species' genomes using GC content.  ... 
doi:10.1093/nar/gku378 pmid:24829449 pmcid:PMC4066789 fatcat:s3ld35na5vdftgmya2wpiyl4vy

HGTree: database of horizontally transferred genes determined by tree reconciliation

Hyeonsoo Jeong, Samsun Sung, Taehyung Kwon, Minseok Seo, Kelsey Caetano-Anollés, Sang Ho Choi, Seoae Cho, Arshan Nasir, Heebal Kim
2015 Nucleic Acids Research  
The HGTree database provides putative genomewide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes.  ...  In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand  ...  Thanks are also extended to members of BIOPOP, Seoul National University and members of Functional Genomics laboratory, COM-SATS Institute of Information Technology, Islamabad for their kind support.  ... 
doi:10.1093/nar/gkv1245 pmid:26578597 pmcid:PMC4702880 fatcat:woxhoski2ffubleeyt7bzrxw6m

On detection and assessment of statistical significance of Genomic Islands

Raghunath Chatterjee, Keya Chaudhuri, Probal Chaudhuri
2008 BMC Genomics  
Some 'putative GIs' are identified in the first phase, and those are refined into smaller segments containing horizontally acquired genes in the refinement phase.  ...  Many of the available methods for detecting Genomic Islands (GIs) in prokaryotic genomes use markers such as transposons, proximal tRNAs, flanking repeats etc., or they use other supervised techniques  ...  Acknowledgements The research of Raghunath Chatterjee was supported by a fellowship from the Council of Scientific and Industrial Research, Government of India.  ... 
doi:10.1186/1471-2164-9-150 pmid:18380895 pmcid:PMC2362129 fatcat:rqqvocmrqjfc3oh5cxnbhqmctq

Gene silencing and large-scale domain structure of the E. coli genome

Mina Zarei, Bianca Sclavi, Marco Cosentino Lagomarsino
2013 Molecular Biosystems  
to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer.  ...  The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression.  ...  Supplementary Table 11 shows the results of systematic hypergeometric testing for enrichment of MultiFun functional categories within the lists of functional genes located in each cluster that is reported  ... 
doi:10.1039/c3mb25364c pmid:23412141 fatcat:wjxodwomzvghfdjkrgtfwdp4se

Gene silencing and large-scale domain structure of the E. coli genome [article]

Mina Zarei, Bianca Sclavi, Marco Cosentino Lagomarsino
2012 arXiv   pre-print
to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer.  ...  The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression.  ...  Supplementary Table 11 shows the results of systematic hypergeometric testing for enrichment of MultiFun functional categories within the lists of functional genes located in each cluster that is reported  ... 
arXiv:1209.6513v1 fatcat:tr22kgh52nbfxobtjn2cbjhpu4
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