Vector Embeddings by Sequence Similarity and Context for Improved Compression, Similarity Search, Clustering, Organization, and Manipulation of cDNA Libraries. (arXiv:2308.05118v1 [q-bio.GN])

This paper demonstrates the utility of organized numerical representations of
genes in research involving flat string gene formats (i.e., FASTA/FASTQ5).
FASTA/FASTQ files have several current limitations, such as their large file
sizes, slow processing speeds for mapping and alignment, and contextual
dependencies. These challenges significantly hinder investigations and tasks
that involve finding similar sequences. The solution lies in transforming
sequences into an alternative representation that facilitates easier clustering
into similar groups compared to the raw sequences themselves. By assigning a …

alignment arxiv bio clustering compression context current embeddings files gene genes libraries limitations manipulation mapping numerical organization paper processing research search string utility vector vector embeddings