Evidence map›Paper›PMID 28187714›Full record

ArticleBMC bioinformatics2017

TipMT: Identification of PCR-based taxon-specific markers.

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

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.7field-weighted citation impact, top 24% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 4 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 3 institutions in 1 country.

Gabriela F Rodrigues-LuizLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Mariana S CardosoLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Hugo O ValdiviaLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Edward V AyalaLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Célia M F GontijoCentro de Pesquisa René Rachou, Fiocruz, Belo Horizonte, Brazil.
Thiago de S RodriguesDepartamento de Computação, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Ricardo T FujiwaraLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Robson S LopesLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Daniella C BartholomeuLaboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. daniella@icb.ufmg.br.
Universidade Federal de Minas Gerais · BRFederal Center for Technological Education of Minas Gerais · BRFundação Oswaldo Cruz · BR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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/ .

Indexed as

Polymerase Chain ReactionUser-Computer InterfaceDNA PrimersGenetic MarkersGenome, ProtozoanInternetLeishmaniaDNA PrimersGenetic MarkersMolecular markerPCRPCR MultiplexSpecific primersWeb application

Identifiers

PMID28187714
PMCPMC5303226
OpenAlexW2587506305

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.