In this work we propose an approach to improve the performance of a current methodology, computing k-mer based sequence similarity via Jaccard index, for pangenomic analyses. Recent studies have shown a good performance of such a measure for retrieving homology among genetic sequences belonging to a group of genomes. Our improvement is obtained by exploiting a suitable k-mer representation, which enables a fast and memory-cheap computation of sequence similarity. Experimental results on genomes of living organisms of different species give an evidence that a state of the art methodology is here improved, in terms of running time and memory requirements.

A k-mer Based Sequence Similarity for Pangenomic Analyses / Bonnici, V.; Cracco, A.; Franco, G.. - 13164(2022), pp. 31-44. [10.1007/978-3-030-95470-3_3]

A k-mer Based Sequence Similarity for Pangenomic Analyses

Bonnici V.
;
2022

Abstract

In this work we propose an approach to improve the performance of a current methodology, computing k-mer based sequence similarity via Jaccard index, for pangenomic analyses. Recent studies have shown a good performance of such a measure for retrieving homology among genetic sequences belonging to a group of genomes. Our improvement is obtained by exploiting a suitable k-mer representation, which enables a fast and memory-cheap computation of sequence similarity. Experimental results on genomes of living organisms of different species give an evidence that a state of the art methodology is here improved, in terms of running time and memory requirements.
A k-mer Based Sequence Similarity for Pangenomic Analyses / Bonnici, V.; Cracco, A.; Franco, G.. - 13164(2022), pp. 31-44. [10.1007/978-3-030-95470-3_3]
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11381/2919531
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 1
  • ???jsp.display-item.citation.isi??? ND
social impact