TipMT: Identification of PCR-based taxon-specific markers

BMC Bioinformatics

Software

Célia M. F. Gontijo¹  Thiago de S. Rodrigues²  Gabriela F. Rodrigues-Luiz³  Hugo O. Valdivia³  Ricardo T. Fujiwara³  Edward V. Ayala³  Daniella C. Bartholomeu³  Mariana S. Cardoso³  Robson S. Lopes⁴ 

[1] Centro de Pesquisa René Rachou, Fiocruz, Belo Horizonte, Brazil;Departamento de Computação, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil;Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil;Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil;Departamento de Computação, Universidade Federal do Mato Grosso, Barra do Garças, Mato Grosso, Brazil;

关键词: Molecular marker;    Specific primers;    PCR;    PCR Multiplex;    Web application;   

DOI  :  10.1186/s12859-017-1485-3

 received in 2016-06-16, accepted in 2017-01-11,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMolecular 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.ResultsHere, 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.ConclusionsThe 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/.

【 授权许可】

CC BY   
© The Author(s). 2017