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. 2017 Feb 11;18(1):104.
doi: 10.1186/s12859-017-1485-3.

TipMT: Identification of PCR-based taxon-specific markers

Gabriela F Rodrigues-Luiz  1 , Mariana S Cardoso  1 , Hugo O Valdivia  1 , Edward V Ayala  1 , Célia M F Gontijo  2 , Thiago de S Rodrigues  3 , Ricardo T Fujiwara  1 , Robson S Lopes  1   4 , Daniella C Bartholomeu  5
Affiliations

TipMT: Identification of PCR-based taxon-specific markers

Gabriela F Rodrigues-Luiz et al. BMC Bioinformatics. .

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/ .

Keywords: Molecular marker; PCR; PCR Multiplex; Specific primers; Web application.

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Figures

Fig. 1
Fig. 1
Flowchart for TipMT analysis
Fig. 2
Fig. 2
Real and virtual (e-MPX) gel electrophoresis for specific G1 pairs of primers (a and b) and single S1 pair of primers (c). Each lane corresponds to the combination of genomic DNA of Leishmania species and pair of primers identified at the top of the gel (standard PCR in a and c and multiplex PCR in b). La: L. amazonensis; Lb: L. braziliensis; Li: L. infantum; Lm: L. major; gDNA: genomic DNA; bp: base pair
See this image and copyright information in PMC

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