CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase.

ABSTRACT:

Motivation

Rapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based on k-mer frequencies offers a computationally efficient solution, yet in practice, the k-mer frequency vectors for large k of practical interest lead to excessive memory and storage consumption.

Results

We report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequen

SUBMITTER: Lu YY 

PROVIDER: S-EPMC9431648 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature