Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F19%3APU131157" target="_blank" >RIV/00216305:26220/19:PU131157 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/65269705:_____/19:00070876 RIV/00216224:14110/19:00110574

Výsledek na webu

<a href="http://www.sciencedirect.com/science/article/pii/S2090123219300050" target="_blank" >http://www.sciencedirect.com/science/article/pii/S2090123219300050</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jare.2019.01.005" target="_blank" >10.1016/j.jare.2019.01.005</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data

Popis výsledku v původním jazyce

Large-scale comparative studies of DNA fingerprints prefer automated chip capillary electrophoresis over conventional gel planar electrophoresis due to the higher precision of the digitalization process. However, the determination of band sizes is still limited by the device resolution and sizing accuracy. Band matching, therefore, remains the key step in DNA fingerprint analysis. Most current methods evaluate only the pairwise similarity of the samples, using heuristically determined constant thresholds to evaluate the maximum allowed band size deviation; unfortunately, that approach significantly reduces the ability to distinguish between closely related samples. This study presents a new approach based on global multiple alignments of bands of all samples, with an adaptive threshold derived from the detailed migration analysis of a large number of real samples. The proposed approach allows the accurate automated analysis of DNA fingerprint similarities for extensive epidemiological studies of bacterial strains, thereby helping to prevent the spread of dangerous microbial infections.

Název v anglickém jazyce

Advanced DNA fingerprint genotyping based on a model developed from real chip electrophoresis data

Popis výsledku anglicky

Large-scale comparative studies of DNA fingerprints prefer automated chip capillary electrophoresis over conventional gel planar electrophoresis due to the higher precision of the digitalization process. However, the determination of band sizes is still limited by the device resolution and sizing accuracy. Band matching, therefore, remains the key step in DNA fingerprint analysis. Most current methods evaluate only the pairwise similarity of the samples, using heuristically determined constant thresholds to evaluate the maximum allowed band size deviation; unfortunately, that approach significantly reduces the ability to distinguish between closely related samples. This study presents a new approach based on global multiple alignments of bands of all samples, with an adaptive threshold derived from the detailed migration analysis of a large number of real samples. The proposed approach allows the accurate automated analysis of DNA fingerprint similarities for extensive epidemiological studies of bacterial strains, thereby helping to prevent the spread of dangerous microbial infections.

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/GA17-01821S" target="_blank" >GA17-01821S: Výkonnostní techniky pro sestavování a anotaci bakteriálního genomu využívající číslicové zpracování genomických signálů</a><br>

Návaznosti

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

Rok uplatnění

2019

Kód důvěrnosti údajů

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

Název periodika

Journal of Advanced Research

ISSN

2090-1232

e-ISSN

—

Svazek periodika

18

Číslo periodika v rámci svazku

18

Stát vydavatele periodika

EG - Egyptská arabská republika

Počet stran výsledku

10

Strana od-do

9-18

Kód UT WoS článku

000471218900002

EID výsledku v databázi Scopus

2-s2.0-85061153550