title: TipMT: Identification of PCR-based taxon-specific markers.
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/ .
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Gabriela F
authors.initials: GF
authors.lastname: Rodrigues-Luiz
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Mariana S
authors.initials: MS
authors.lastname: Cardoso
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Hugo O
authors.initials: HO
authors.lastname: Valdivia
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Edward V
authors.initials: EV
authors.lastname: Ayala
authors.affiliation: Centro de Pesquisa René Rachou, Fiocruz, Belo Horizonte, Brazil.
authors.forename: Célia M F
authors.initials: CM
authors.lastname: Gontijo
authors.affiliation: Departamento de Computação, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Thiago de S
authors.initials: TS
authors.lastname: Rodrigues
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
authors.forename: Ricardo T
authors.initials: RT
authors.lastname: Fujiwara
authors.affiliation: 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.
authors.forename: Robson S
authors.initials: RS
authors.lastname: Lopes
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. daniella@icb.ufmg.br.
authors.forename: Daniella C
authors.initials: DC
authors.lastname: Bartholomeu
mesh_terms: D017931:DNA Primers / Q000737:chemistry / Q000378:metabolism*; D005819:Genetic Markers / Q000235:genetics*; D018503:Genome, Protozoan; D020407:Internet; D007891:Leishmania / Q000235:genetics; D016133:Polymerase Chain Reaction; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers; D005819:Genetic Markers
keywords: Molecular marker; PCR; PCR Multiplex; Specific primers; Web application