LUCApedia: a database for the study of ancient life

Nucleic Acids Research
Aaron David GoldmanLaura F Landweber

Abstract

Organisms represented by the root of the universal evolutionary tree were most likely complex cells with a sophisticated protein translation system and a DNA genome encoding hundreds of genes. The growth of bioinformatics data from taxonomically diverse organisms has made it possible to infer the likely properties of early life in greater detail. Here we present LUCApedia, (http://eeb.princeton.edu/lucapedia), a unified framework for simultaneously evaluating multiple data sets related to the Last Universal Common Ancestor (LUCA) and its predecessors. This unification is achieved by mapping eleven such data sets onto UniProt, KEGG and BioCyc IDs. LUCApedia may be used to rapidly acquire evidence that a certain gene or set of genes is ancient, to examine the early evolution of metabolic pathways, or to test specific hypotheses related to ancient life by corroborating them against the rest of the database.

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Citations

Feb 11, 2014·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Ian S Dunn
Jun 14, 2013·The Journal of Endocrinology·Gina L C YostenWillis K Samson
Jan 7, 2016·Journal of Molecular Evolution·Aaron David GoldmanLaura F Landweber
Nov 20, 2015·Journal of Molecular Evolution·Anthony M PooleDavid Penny
Nov 27, 2014·Journal of Molecular Evolution·Anthony M PooleJun Ogawa
May 25, 2015·Trends in Genetics : TIG·Stephen Richards
Sep 13, 2013·Chemical Reviews·Finn Werner
Nov 12, 2017·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Miryam Palacios-PérezMarco V José
Sep 4, 2014·Microbiology and Molecular Biology Reviews : MMBR·Joana C XavierIsabel Rocha
Nov 30, 2018·Annual Review of Animal Biosciences·Jose V LopezIliana B Baums
May 28, 2019·Life·Tian TianHong-Yu Zhang
Feb 16, 2020·Journal of Molecular Evolution·David A LiberlesAndrew Storfer
Mar 1, 2020·Life·Martina PreinerJoana C Xavier
Apr 22, 2020·Molecular Biology and Evolution·Sarah J Berkemer, Shawn E McGlynn
Aug 19, 2020·Journal of Molecular Evolution·Yuta A TakagiAaron D Goldman
Nov 6, 2015·Frontiers in Microbiology·Anthony M PooleKalle T Rytkönen
Nov 26, 2016·Nature Microbiology·Johann Peter Gogarten, David Deamer
Feb 7, 2021·Journal of Molecular Evolution·Aaron D Goldman, Betul Kacar
Mar 7, 2017·Cell·Joshua E GoldfordDaniel Segrè

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Software Mentioned

MySQL
BLAST
LUCApedia
BioCyc

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