Cargando…

MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants

MOTIVATION: Bloom filters are a popular data structure that allows rapid searches in large sequence datasets. So far, all tools work with nucleotide sequences; however, protein sequences are conserved over longer evolutionary distances, and only mutations on the protein level may have any functional...

Descripción completa

Detalles Bibliográficos
Autores principales: Srikakulam, Sanjay K, Keller, Sebastian, Dabbaghie, Fawaz, Bals, Robert, Kalinina, Olga V
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9994790/
https://www.ncbi.nlm.nih.gov/pubmed/36825843
http://dx.doi.org/10.1093/bioinformatics/btad101
Descripción
Sumario:MOTIVATION: Bloom filters are a popular data structure that allows rapid searches in large sequence datasets. So far, all tools work with nucleotide sequences; however, protein sequences are conserved over longer evolutionary distances, and only mutations on the protein level may have any functional significance. RESULTS: We present MetaProFi, a Bloom filter-based tool that, for the first time, offers the functionality to build indexes of amino acid sequences and query them with both amino acid and nucleotide sequences, thus bringing sequence comparison to the biologically relevant protein level. MetaProFi implements additional efficient engineering solutions, such as a shared memory system, chunked data storage and efficient compression. In addition to its conceptual novelty, MetaProFi demonstrates state-of-the-art performance and excellent memory consumption-to-speed ratio when applied to various large datasets. AVAILABILITY AND IMPLEMENTATION: Source code in Python is available at https://github.com/kalininalab/metaprofi.