Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation

Patrick V. Phaneuf, Dennis Gosting, Bernhard O. Palsson, Adam M. Feist*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotypephenotype relationships, but also allows for the revelation of the series of genetic alterations required to acquire the new phenotype. Numerous ALE studies have been published, providing a strong impetus for developing databases to warehouse experimental evolution information and make it retrievable for large-scale analysis. Here, the first step towards establishing this resource is presented: ALEdb (http: //aledb.org). This initial release contains over 11 000 mutations that have been discovered from eleven ALE publications. ALEdb (i) is a web-based platform that comprehensively reports on ALE acquired mutations and their conditions, (ii) reports key mutations using previously established trends, (iii) enables a search-driven workflow to enhance user mutation functional analysis through mutation crossreference, (iv) allows exporting of mutation query results for custom analysis, (v) includes a bibliome describing the databased experiment publications and (vi) contains experimental evolution mutations from multiple model organisms. Thus, ALEdb is an informative platform which will become increasingly revealing as the number of reported ALE experiments and identified mutations continue to expand.

Original languageEnglish
Article numbergky983
JournalNucleic acids research
Volume47
Issue numberD1
Pages (from-to)D1164-D1171
Number of pages8
ISSN0305-1048
DOIs
Publication statusPublished - 2019

Cite this

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title = "Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation",
abstract = "Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotypephenotype relationships, but also allows for the revelation of the series of genetic alterations required to acquire the new phenotype. Numerous ALE studies have been published, providing a strong impetus for developing databases to warehouse experimental evolution information and make it retrievable for large-scale analysis. Here, the first step towards establishing this resource is presented: ALEdb (http: //aledb.org). This initial release contains over 11 000 mutations that have been discovered from eleven ALE publications. ALEdb (i) is a web-based platform that comprehensively reports on ALE acquired mutations and their conditions, (ii) reports key mutations using previously established trends, (iii) enables a search-driven workflow to enhance user mutation functional analysis through mutation crossreference, (iv) allows exporting of mutation query results for custom analysis, (v) includes a bibliome describing the databased experiment publications and (vi) contains experimental evolution mutations from multiple model organisms. Thus, ALEdb is an informative platform which will become increasingly revealing as the number of reported ALE experiments and identified mutations continue to expand.",
author = "Phaneuf, {Patrick V.} and Dennis Gosting and Palsson, {Bernhard O.} and Feist, {Adam M.}",
year = "2019",
doi = "10.1093/nar/gky983",
language = "English",
volume = "47",
pages = "D1164--D1171",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
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}

Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation. / Phaneuf, Patrick V.; Gosting, Dennis; Palsson, Bernhard O.; Feist, Adam M.

In: Nucleic acids research, Vol. 47, No. D1, gky983, 2019, p. D1164-D1171.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation

AU - Phaneuf, Patrick V.

AU - Gosting, Dennis

AU - Palsson, Bernhard O.

AU - Feist, Adam M.

PY - 2019

Y1 - 2019

N2 - Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotypephenotype relationships, but also allows for the revelation of the series of genetic alterations required to acquire the new phenotype. Numerous ALE studies have been published, providing a strong impetus for developing databases to warehouse experimental evolution information and make it retrievable for large-scale analysis. Here, the first step towards establishing this resource is presented: ALEdb (http: //aledb.org). This initial release contains over 11 000 mutations that have been discovered from eleven ALE publications. ALEdb (i) is a web-based platform that comprehensively reports on ALE acquired mutations and their conditions, (ii) reports key mutations using previously established trends, (iii) enables a search-driven workflow to enhance user mutation functional analysis through mutation crossreference, (iv) allows exporting of mutation query results for custom analysis, (v) includes a bibliome describing the databased experiment publications and (vi) contains experimental evolution mutations from multiple model organisms. Thus, ALEdb is an informative platform which will become increasingly revealing as the number of reported ALE experiments and identified mutations continue to expand.

AB - Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotypephenotype relationships, but also allows for the revelation of the series of genetic alterations required to acquire the new phenotype. Numerous ALE studies have been published, providing a strong impetus for developing databases to warehouse experimental evolution information and make it retrievable for large-scale analysis. Here, the first step towards establishing this resource is presented: ALEdb (http: //aledb.org). This initial release contains over 11 000 mutations that have been discovered from eleven ALE publications. ALEdb (i) is a web-based platform that comprehensively reports on ALE acquired mutations and their conditions, (ii) reports key mutations using previously established trends, (iii) enables a search-driven workflow to enhance user mutation functional analysis through mutation crossreference, (iv) allows exporting of mutation query results for custom analysis, (v) includes a bibliome describing the databased experiment publications and (vi) contains experimental evolution mutations from multiple model organisms. Thus, ALEdb is an informative platform which will become increasingly revealing as the number of reported ALE experiments and identified mutations continue to expand.

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