BIMSA > Seminar on Bioinformatics A improvement for whole genome phylogenetic analysis using Fourier transform by leading into kmer
A improvement for whole genome phylogenetic analysis using Fourier transform by leading into kmer
Organizer
Shing Toung Yau
Speaker
Mengcen Guan
Time
Thursday, October 19, 2023 9:00 PM - 9:30 PM
Venue
Online
Abstract
Prof. Yin used Fourier transform (time series converted into frequency spectrum) to study the evolutionary relationships of whole genomes, especially mentioned that compared to the multiple alignment method and the ordinary 4-d Fourier, the improved 2-d method can distinguish between insertion, deletion, and so on. Considering kmer, it is more sensitive to deletion than individual ATCG. For 2mer, there are 16 types of 2mer: AA, AT, AC, AG,..., GA, GT, GG , which are naturally transformed into mathematical signals through a 4-dimensional hypercube with 16 vertices. I tested this idea.