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HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
2003
Nucleic Acids Research
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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
2008
Nucleic Acids Research
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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
2005
Research in Microbiology
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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
2007
Molecular biology and evolution
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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
2005
BMC Genomics
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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
2006
Computer applications in the biosciences : CABIOS
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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
2011
PLoS ONE
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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
2010
BMC Bioinformatics
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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
2006
Nucleic Acids Research
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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
2010
Proceedings of the 2010 ACM Symposium on Applied Computing - SAC '10
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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
2014
Nucleic Acids Research
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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
2015
Nucleic Acids Research
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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
2008
BMC Genomics
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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
2013
Molecular Biosystems
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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]
2012
arXiv
pre-print
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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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