Unraveling the Power of Genetic Sequences from Whole Genomes: A Pathway to Understanding Insect Detoxification
This Python-based genomic data analysis aims to enhance our understanding of these essential genetic sequences and their implications in insect detoxification mechanisms. The main objectives are:
1. Develop a function to efficiently extract genes of interest from one or more genomes. GeneFind.py looks for genes in one or several genomes. The sequences found are renamed using the file name where they were found and are appended to a file.
2. Implement a function to filter sequences to the desired base pair (bp) length for targeted analysis. SeqFilter.py filters sequences with a user-defined threshold and creates two files, one containing sequences that have passed the threshold and one with sequences that did not.
3. Utilize MAFFT to align the retrieved sequences for accurate comparisons.
4. Generate and visualize gene trees to gain valuable insights.
Focus Gene: ATPase Alpha Subunit The ATPase alpha subunit plays a crucial role in the detoxification process employed by insects against toxic substances present in the plants they consume. Our analysis will encompass eighteen genomes of milkweed longhorn beetles, as well as other insect orders such as butterflies and true bugs.