DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes

Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners

This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-fixed dimensions, which correspond to the length of the sequences. Through computational procedures such as one-hot encoding, numerical encoding plays an important role in DNA sequence evaluation (OHE). However, the OHE method has some disadvantages: (1) It does not add any details that could result in an additional predictive variable, and (2) if the variable has many classes, OHE significantly expands the feature space. To address these shortcomings, this chapter proposes a computationally efficient framework for classifying DNA sequences of living organisms in the image domain. A multilayer perceptron trained by a pseudoinverse learning autoencoder (PILAE) algorithm is used in the proposed strategy. The learning control parameters and the number of hidden layers do not have to be specified during the PILAE training process. As a result, the PILAE classifier outperforms other deep neural network (DNN) strategies such as the VGG-16 and Xception models.

FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments

Researchers seldom look at naked genome assemblies: instead the attributes of DNA sequences are mediated through statistics, annotations and high level summaries. Here we present software that visualizes the bare sequences of whole genome assemblies in a zoomable interface. This can assist in detection of chromosome architecture and contamination by the naked eye through changes in color patterns, in the absence of any other annotation. When available, annotations can be visualized alongside or on top of the naked sequence. Genome alignments can also be visualized, laying two genomes side by side in an alignment and highlighting their differences at nucleotide resolution. FluentDNA gives researchers direct visualization of whole genome assemblies, annotations and alignments, for quality control, hypothesis generation, and communicating results.