| Author | Luiz, Gabriela Flávia Rodrigues | |
| Author | Cardoso, Mariana Santos | |
| Author | Valdivia, Hugo Oswaldo | |
| Author | Ayala, Edward Valencia | |
| Author | Gontijo, Célia Maria Ferreira | |
| Author | Rodrigues, Thiago de Souza | |
| Author | Fujiwara, Ricardo Toshio | |
| Author | Lopes, Robson da Silva | |
| Author | Bartholomeu, Daniella Castanheira | |
| Access date | 2018-06-06T18:45:09Z | |
| Available date | 2018-06-06T18:45:09Z | |
| Document date | 2017 | |
| Citation | LUIZ, Gabriela Flávia Rodrigues et al. TipMT: Identification of PCR-based taxon-specific markers. BMC Bioinformatic., v. 18, n. 1, 104, 2017 | pt_BR |
| ISSN | 1471-2105 | pt_BR |
| URI | https://www.arca.fiocruz.br/handle/icict/26753 | |
| Language | eng | pt_BR |
| Publisher | BioMed Central | pt_BR |
| Rights | restricted access | pt_BR |
| Subject in Portuguese | marcadores moleculares | pt_BR |
| Subject in Portuguese | PCR Multiplex | pt_BR |
| Title | TipMT: Identification of PCR-based taxon-specific markers. | pt_BR |
| Type | Article | |
| DOI | 10.1186/s12859-017-1485-3 | |
| Abstract | Background: Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity.
Results: Here, we report the development of a Tool for Identification of Primers for Multiple Taxa (TipMT), which is a web application to search and design primers for genotyping based on genomic data. The tool identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using Multiplex PCR. This pipeline was applied to the genomes of four species of Leishmania (L. amazonensis, L. braziliensis, L. infantum and L. major) and validated by PCR using artificial genomic DNA mixtures of the Leishmania species as templates. This experimental validation demonstrates the reliability of TipMT because amplification profiles showed discrimination of genomic DNA samples from Leishmania species.
Conclusions: The TipMT web tool allows for large-scale identification and design of taxon-specific primers and is freely available to the scientific community at http://200.131.37.155/tipMT/. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil | pt_BR |
| Affilliation | Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil. | pt_BR |
| Affilliation | Centro Federal de Educação Tecnológica de Minas Gerais. Departamento de Computação. Belo Horizonte, MG, Brazil. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil/Universidade Federal do Mato Grosso. Departamento de Computação. Barra do Garças, MT, Brazil. | pt_BR |
| Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Imunologia e Genômica de Parasitos. Belo Horizonte, MG, Brazil | pt_BR |
| Subject | Molecular marker | pt_BR |
| Subject | Specific primers | pt_BR |
| Subject | PCR | pt_BR |
| Subject | PCR Multiplex | pt_BR |
| Subject | Web application | pt_BR |
| Embargo date | 2022-01-01 | |
