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PARSID: a Python script for automatic analysis of local BLAST results for a rapid molecular taxonomic identification.
Piccoli, Costanza; Muñoz-Mérida, Antonio; Crottini, Angelica.
Afiliación
  • Piccoli C; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal. costanza.piccoli.92@gmail.com.
  • Muñoz-Mérida A; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169- 007, Porto, Portugal. costanza.piccoli.92@gmail.com.
  • Crottini A; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal. costanza.piccoli.92@gmail.com.
BMC Res Notes ; 17(1): 35, 2024 Jan 24.
Article en En | MEDLINE | ID: mdl-38268047
ABSTRACT

OBJECTIVE:

A reliable taxonomic identification of species from molecular samples is the first step for many studies. For researchers unfamiliar with programming, running a BLAST analysis, filtering, and organizing results for hundreds of sequences through the BLAST web interface can be difficult. Additionally, sequences deposited in GenBank can have outdated taxonomic identification. The use of reliable Reference Sequences Library (RSL) containing accurate taxonomically-identified sequences facilitates this task. Pending the availability of a RSL with the user, we developed a tool that automates the molecular taxonomic identification of sequences.

RESULTS:

We developed PARSID, a Python script running through the command-line that automates the routine workflow of blasting an input sequence file against the user's RSL, and retrieves the matches with the highest percentage of identity in five steps. PARSID accepts cut-off parameters and supplementary information in a.csv file for filtering the results. The final output is visualized in a spreadsheet. We tested its functioning using 10 input sequences simulating different situations of the molecular taxonomic identification of sequences against an example RSL containing 25 sequences. Step-by-step instructions and test files are publicly available at https//github.com/kokinide/PARSID.git .
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Publicaciones / Bases de Datos de Ácidos Nucleicos Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: BMC Res Notes Año: 2024 Tipo del documento: Article País de afiliación: Portugal Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Publicaciones / Bases de Datos de Ácidos Nucleicos Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: BMC Res Notes Año: 2024 Tipo del documento: Article País de afiliación: Portugal Pais de publicación: Reino Unido