Finding Maximal Exact Matches Using the r-Index.
J Comput Biol
; 29(2): 188-194, 2022 02.
Article
em En
| MEDLINE
| ID: mdl-35041518
ABSTRACT
Efficiently finding maximal exact matches (MEMs) between a sequence read and a database of genomes is a key first step in read alignment. But until recently, it was unknown how to build a data structure in [Formula see text] space that supports efficient MEM finding, where r is the number of runs in the Burrows-Wheeler Transform. In 2021, Rossi et al. showed how to build a small auxiliary data structure called thresholds in addition to the r-index in [Formula see text] space. This addition enables efficient MEM finding using the r-index. In this article, we present the tool that implements this solution, which we call MONI. Namely, we give a high-level view of the main components of the data structure and show how the source code can be downloaded, compiled, and used to find MEMs between a set of sequence reads and a set of genomes.
Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Software
/
Alinhamento de Sequência
Tipo de estudo:
Diagnostic_studies
Limite:
Humans
Idioma:
En
Revista:
J Comput Biol
Assunto da revista:
BIOLOGIA MOLECULAR
/
INFORMATICA MEDICA
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Estados Unidos