Research output per year
Research output per year
Description
Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations
We use data from NCBI RefSeq (see prokaryotes.csv) in amino acid format. From the NCBI genome list, FTP URLs are shown to download the files. The amino acid format files end in "_protein.faa.gz".
The list of genomes we used for the testing of the minimisation of the number of Lyndon factors and balancing the length of Lyndon factors is in testingGenomeList. The name of the genome we used for finding the mutation operator to use for the EA is in trainingGenome.
In our code, ModifiedDuvals was the working name of Flexi-Duval. Similarly, ModifiedDuvalsOperator refers to the LF-inspired operator.
NCBI have reduced the number of reference genomes https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/14/assembly-changes/.
We use data from NCBI RefSeq (see prokaryotes.csv) in amino acid format. From the NCBI genome list, FTP URLs are shown to download the files. The amino acid format files end in "_protein.faa.gz".
The list of genomes we used for the testing of the minimisation of the number of Lyndon factors and balancing the length of Lyndon factors is in testingGenomeList. The name of the genome we used for finding the mutation operator to use for the EA is in trainingGenome.
In our code, ModifiedDuvals was the working name of Flexi-Duval. Similarly, ModifiedDuvalsOperator refers to the LF-inspired operator.
NCBI have reduced the number of reference genomes https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/14/assembly-changes/.
| Date made available | 05 Sept 2020 |
|---|---|
| Publisher | Prifysgol Aberystwyth | Aberystwyth University |
| Date of data production | 27 May 2020 |
Research output
- 1 Conference Proceeding (Non-Journal item)
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Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations
Major, L., Clare, A., Daykin, J., Mora, B., Peña Gamboa, L. & Zarges, C., 31 Aug 2020, Parallel Problem Solving from Nature – PPSN XVI - 16th International Conference, PPSN 2020, Proceedings: 16th International Conference, Leiden, The Netherlands, September 5-9, 2020, Proceedings. Bäck, T., Preuss, M., Deutz, A., Emmerich, M., Wang, H., Doerr, C. & Trautmann, H. (eds.). Springer Nature, p. 390-403 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12269 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (Non-Journal item)
Open AccessFile3 Citations (Scopus)172 Downloads (Pure)
Datasets
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Supporting Information for Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations - Code
Major, L., Clare, A., Daykin, J., Mora, B., Peña Gamboa, L. & Zarges, C., Prifysgol Aberystwyth | Aberystwyth University, 05 Sept 2020
DOI: 10.5281/zenodo.3896389, https://github.com/jam86/Evaluation-of-a-Permutation-Based-Evolutionary-Framework-for-Lyndon-Factorizations
Dataset