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

ABSTRACT:

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,

SUBMITTER: Srikakulam SK 

PROVIDER: S-EPMC9994790 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature