Reference-free phylogeny from sequencing data

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21230%2F23%3A00365342" target="_blank" >RIV/68407700:21230/23:00365342 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1186/s13040-023-00329-x" target="_blank" >https://doi.org/10.1186/s13040-023-00329-x</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13040-023-00329-x" target="_blank" >10.1186/s13040-023-00329-x</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Reference-free phylogeny from sequencing data

Popis výsledku v původním jazyce

Motivation Clustering of genetic sequences is one of the key parts of bioinformatics analyses. Resulting phylogenetic trees are beneficial for solving many research questions, including tracing the history of species, studying migration in the past, or tracing a source of a virus outbreak. At the same time, biologists provide more data in the raw form of reads or only on contig-level assembly. Therefore, tools that are able to process those data without supervision need to be developed. Results In this paper, we present a tool for reference-free phylogeny capable of handling data where no mature-level assembly is available. The tool allows distance calculation for raw reads, contigs, and the combination of the latter. The tool provides an estimation of the Levenshtein distance between the sequences, which in turn estimates the number of mutations between the organisms. Compared to the previous research, the novelty of the method lies in a newly proposed combination of the read and contig measures, a new method for read-contig mapping, and an efficient embedding of contigs.

Název v anglickém jazyce

Reference-free phylogeny from sequencing data

Popis výsledku anglicky

Motivation Clustering of genetic sequences is one of the key parts of bioinformatics analyses. Resulting phylogenetic trees are beneficial for solving many research questions, including tracing the history of species, studying migration in the past, or tracing a source of a virus outbreak. At the same time, biologists provide more data in the raw form of reads or only on contig-level assembly. Therefore, tools that are able to process those data without supervision need to be developed. Results In this paper, we present a tool for reference-free phylogeny capable of handling data where no mature-level assembly is available. The tool allows distance calculation for raw reads, contigs, and the combination of the latter. The tool provides an estimation of the Levenshtein distance between the sequences, which in turn estimates the number of mutations between the organisms. Compared to the previous research, the novelty of the method lies in a newly proposed combination of the read and contig measures, a new method for read-contig mapping, and an efficient embedding of contigs.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/EF16_019%2F0000765" target="_blank" >EF16_019/0000765: Výzkumné centrum informatiky</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

BioData Mining

ISSN

1756-0381

e-ISSN

—

Svazek periodika

2023

Číslo periodika v rámci svazku

16

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

20

Strana od-do

—

Kód UT WoS článku

000957539200001

EID výsledku v databázi Scopus

2-s2.0-85151333193