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ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

P. S. Novichkov, I. Ratnere, Y. I. Wolf, E. V. Koonin, I. Dubchak
<span title="2009-01-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution.  ...  Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process.  ...  ACKNOWLEDGEMENTS This work was part of the Virtual Institute for Microbial Stress and Survival (http://VIMSS.lbl.gov).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn684">doi:10.1093/nar/gkn684</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18845571">pmid:18845571</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2686458/">pmcid:PMC2686458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rybwc2blrzcstft4kth4ajyob4">fatcat:rybwc2blrzcstft4kth4ajyob4</a> </span>
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Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

P. S. Novichkov, Y. I. Wolf, I. Dubchak, E. V. Koonin
<span title="2008-10-31">2008</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fu4cl5wxynclfn3telu2mfbrna" style="color: black;">Journal of Bacteriology</a> </i> &nbsp;
On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective  ...  In order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs).  ...  ACKNOWLEDGMENT The research of P.S.N., Y.I.W., and E.V.K. was supported by the Department of Health and Human Services intramural program (National Library of Medicine, NIH).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jb.01237-08">doi:10.1128/jb.01237-08</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18978059">pmid:18978059</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2612427/">pmcid:PMC2612427</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tjjvv2iqdra7nbrnykfwb37bde">fatcat:tjjvv2iqdra7nbrnykfwb37bde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226094716/http://pdfs.semanticscholar.org/6f8a/5c097a0c8aa0cb7e20d8d35c88856aee6977.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6f/8a/6f8a5c097a0c8aa0cb7e20d8d35c88856aee6977.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jb.01237-08"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612427" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Databases for Microbiologists: TABLE 1

Igor B. Zhulin, W. W. Margolin
<span title="2015-05-26">2015</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fu4cl5wxynclfn3telu2mfbrna" style="color: black;">Journal of Bacteriology</a> </i> &nbsp;
The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.  ...  They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways.  ...  Work in my laboratory is supported by grants GM072285 and DE024463 from the National Institutes of Health.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jb.00330-15">doi:10.1128/jb.00330-15</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26013493">pmid:26013493</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4505447/">pmcid:PMC4505447</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6eyuvuplzjc7ravlhhmk6isg6i">fatcat:6eyuvuplzjc7ravlhhmk6isg6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220071748/http://pdfs.semanticscholar.org/2083/47ec50ab1b02af7d2871d3ac5746995bc453.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/83/208347ec50ab1b02af7d2871d3ac5746995bc453.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jb.00330-15"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4505447" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Disentangling The Effects Of Selection And Loss Bias On Gene Dynamics [article]

Jaime Iranzo, Jose A. Cuesta, Susanna Manrubia, Mikhail I. Katsnelson, Eugene V. Koonin
<span title="2017-05-18">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We combine mathematical modelling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different  ...  An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection.  ...  and a research platform for 599 microevolution of prokaryotes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/139725">doi:10.1101/139725</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tzfplwnpzjfmthebhufhuirhbu">fatcat:tzfplwnpzjfmthebhufhuirhbu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502224612/https://www.biorxiv.org/content/biorxiv/early/2017/05/18/139725.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6d/6e/6d6e4b67c0cccb3955b3027ed256b30d7af2cc0d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/139725"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Reconstruction of the evolution of microbial defense systems

Pere Puigbò, Kira S. Makarova, David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin
<span title="2017-04-04">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/frh6t5i3jveazlshhan2ekhgcq" style="color: black;">BMC Evolutionary Biology</a> </i> &nbsp;
Results: We employed a stochastic birth-and-death model to obtain maximum likelihood estimates of the rates of gain and loss of defense genes in 35 groups of closely related bacterial genomes and one group  ...  Evolution of bacterial and archaeal genomes is a highly dynamic process that involves intensive loss of genes as well as gene gain via horizontal transfer, with a lesser contribution from gene duplication  ...  Availability of data and materials The datasets supporting the conclusions of this article are included within the additional files and available at ftp://ftp.ncbi.nlm.nih.gov/pub/kristensen/ ATGC/.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12862-017-0942-y">doi:10.1186/s12862-017-0942-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28376755">pmid:28376755</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5379612/">pmcid:PMC5379612</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7tgzmkvq2vdybcpg4pmwbkimnm">fatcat:7tgzmkvq2vdybcpg4pmwbkimnm</a> </span>
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