PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome.
BMC Bioinformatics
; 25(1): 189, 2024 May 14.
Article
em En
| MEDLINE
| ID: mdl-38745271
ABSTRACT
BACKGROUND:
The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels.RESULTS:
As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea.CONCLUSIONS:
This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https//gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy .Palavras-chave
Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Bactérias
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Software
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RNA Ribossômico 16S
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Archaea
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Primers do DNA
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Microbiota
Limite:
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Espanha