Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.
Cell Syst
; 7(2): 201-207.e4, 2018 08 22.
Article
en En
| MEDLINE
| ID: mdl-29936185
ABSTRACT
Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6-108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
ARN
/
Análisis de Secuencia de ARN
Límite:
Animals
/
Humans
Idioma:
En
Revista:
Cell Syst
Año:
2018
Tipo del documento:
Article
País de afiliación:
Estados Unidos