MSc projects on Metahueristics Algorithms
Instruction for the reproduction of the experiment:
Required installed Software: Python 3.4 or above Required installed packages: Biopython Bio.Phylo Numpy Matplotlib Scipy Fuzzywuzzy Pandas
Database Download Link: http://www.ncbi.nlm.nih.gov/Entrez The output returned by the Entrez Programming Utilities is typically in XML format. To parse such output, you have several options:
- Use Bio.Entrez’s parser to parse the XML output into a Python object;
- Use the DOM (Document Object Model) parser in Python’s standard library;
- Use the SAX (Simple API for XML) parser in Python’s standard library;
- Read the XML output as raw text, and parse it by string searching and manipulation.
Genome database consists of following dataset— Assembly genome assembly information BioCollections museum, herbaria, and other biorepository collections BioProject biological projects providing data to NCBI BioSample descriptions of biological source materials Clone genomic and cDNA clones dbVar genome structural variation studies Genome genome sequencing projects by organism GSS genome survey sequences Nucleotide DNA and RNA sequences Probe sequence-based probes and primers SNP short genetic variations SRA high-throughput DNA and RNA sequence read archive Taxonomy taxonomic classification and nomenclature catalog
NB: You need to change the code on exact point to read various dataset from ‘Genome’ database. Also need to change parameters to get the result variation. Modular programming is used to deal with such a huge dataset. Genetic Algorithm performs the best when it’s parameters are well tuned. So, there may be some deflection in reproduction of experimental results with the actual results mention in the paper.