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TipMT: Identification of PCR-based taxon-specific markers

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 sp...

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Autores principales: Rodrigues-Luiz, Gabriela F., Cardoso, Mariana S., Valdivia, Hugo O., Ayala, Edward V., Gontijo, Célia M. F., Rodrigues, Thiago de S., Fujiwara, Ricardo T., Lopes, Robson S., Bartholomeu, Daniella C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303226/
https://www.ncbi.nlm.nih.gov/pubmed/28187714
http://dx.doi.org/10.1186/s12859-017-1485-3
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author Rodrigues-Luiz, Gabriela F.
Cardoso, Mariana S.
Valdivia, Hugo O.
Ayala, Edward V.
Gontijo, Célia M. F.
Rodrigues, Thiago de S.
Fujiwara, Ricardo T.
Lopes, Robson S.
Bartholomeu, Daniella C.
author_facet Rodrigues-Luiz, Gabriela F.
Cardoso, Mariana S.
Valdivia, Hugo O.
Ayala, Edward V.
Gontijo, Célia M. F.
Rodrigues, Thiago de S.
Fujiwara, Ricardo T.
Lopes, Robson S.
Bartholomeu, Daniella C.
author_sort Rodrigues-Luiz, Gabriela F.
collection PubMed
description 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1485-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-53032262017-02-15 TipMT: Identification of PCR-based taxon-specific markers Rodrigues-Luiz, Gabriela F. Cardoso, Mariana S. Valdivia, Hugo O. Ayala, Edward V. Gontijo, Célia M. F. Rodrigues, Thiago de S. Fujiwara, Ricardo T. Lopes, Robson S. Bartholomeu, Daniella C. BMC Bioinformatics Software 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-017-1485-3) contains supplementary material, which is available to authorized users. BioMed Central 2017-02-11 /pmc/articles/PMC5303226/ /pubmed/28187714 http://dx.doi.org/10.1186/s12859-017-1485-3 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Rodrigues-Luiz, Gabriela F.
Cardoso, Mariana S.
Valdivia, Hugo O.
Ayala, Edward V.
Gontijo, Célia M. F.
Rodrigues, Thiago de S.
Fujiwara, Ricardo T.
Lopes, Robson S.
Bartholomeu, Daniella C.
TipMT: Identification of PCR-based taxon-specific markers
title TipMT: Identification of PCR-based taxon-specific markers
title_full TipMT: Identification of PCR-based taxon-specific markers
title_fullStr TipMT: Identification of PCR-based taxon-specific markers
title_full_unstemmed TipMT: Identification of PCR-based taxon-specific markers
title_short TipMT: Identification of PCR-based taxon-specific markers
title_sort tipmt: identification of pcr-based taxon-specific markers
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303226/
https://www.ncbi.nlm.nih.gov/pubmed/28187714
http://dx.doi.org/10.1186/s12859-017-1485-3
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