About
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 cross-reference, (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.
ALEdb is open-source under the MIT License. It is hosted and maintained by the Systems Biology Research Group at the University of California, San Diego. The PI and Group leader for the ALE activities at UCSD is Dr. Adam Feist. If you are interested in contributing to it or have general questions about its use, please email, afeist@ucsd.edu.
Data Submission
For data submission, please email Dr Adam Feist Here
How do I cite ALEdb?
When using ALEdb in your research, we kindly ask that you cite the latest publication. Your citation of ALEdb will help us to apply for ongoing funding to maintain this resource.
Phaneuf PV, Gosting D, Palsson BO, Feist AM. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 2018; doi:10.1093/nar/gky983
Mutation data generation
The mutation data presented on this platform was generated using an in-house pipeline that incorporates the BreSeq resquencing pipeline, the GATK Best Practices pipeline, and the CNVnator copy number variation detection tool.
Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using BreSeq. Methods Mol. Biol.
Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, Kling DE, Gauthier LD, Levy-Moonshine A, Roazen D, Shakir K, Thibault J, Chandran S, Whelan C, Lek M, Gabriel S, Daly MJ, Neale B, MacArthur DG, Banks E. (2017). Scaling accurate genetic variant discovery to tens of thousands of samples bioRxiv, 201178.
Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011 Jun;21(6):974-84.
3rd party packages used
mutation-needle-plot: http://dx.doi.org/10.5281/zenodo.14561
License
Copyright © 2015-2026 The Feist Lab
ALEdb is released under the MIT License. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE, OR OTHERWISE ARISING FROM THE USE OR OTHER DEALINGS IN THE SOFTWARE.
