Bioinformatics
Large-scale detection and application of expressed sequence tag single nucleotide polymorphisms in Nicotiana
Authors: Y. Wang, D. Zhou, S. Wang and L. Yang
Single nucleotide polymorphisms (SNPs) are widespread in the Nicotiana genome. Using an alignment and variation detection method, we developed 20,607,973 SNPs, based on the expressed sequence tag sequences of 10 Nicotiana species. The replacement rate was much higher than the transversion rate in the SNPs, and SNPs widely exist in the Nicotiana. In vitro .. Read More»
- Genet. Mol. Res. 14(3):
- 2015.July.14.5
- DOI:
- 10.4238/2015.July.14.5
Cut-and-paste-based cloning strategy for large gene site-directed mutagenesis
Authors: C. Wang, T.Y. Wang, L.Y. Zhang, X.J. Gao, X.W. Wang and C.J. Jin
Site-directed mutagenesis is an essential technique for investigating the mechanisms of gene regulation on a molecular level, as well as for exploring post-translational modifications and functional structure at the protein level. Polymerase chain reaction combining in vitro synthesis of oligonucleotide primers allows for site-directed mutation to be perf.. Read More»
- Genet. Mol. Res. 14(2):
- 2015.May.25.10
- DOI:
- 10.4238/2015.May.25.10
FSHR gene Thr307Ala and Asn680Ser polymorphisms in infertile men: an association study in North China and meta-analysis
Authors: X.Q. Wu, S.M. Xu, Y.Q. Wang, Q. Li, Z.Q. Wang, C.L. Zhang and Y. Shen
Male infertility is a complex multifactorial and polygenic disease, and genetic factors play an important role in its formation and development. Recently, the association between follicle stimulating hormone receptor (FSHR) gene polymorphisms and male infertility risk has attracted widespread attention due to the unique biological functions of FSH. The ai.. Read More»
- Genet. Mol. Res. 14(2):
- 2015.May.25.11
- DOI:
- 10.4238/2015.May.25.11
Polymorphic CA microsatellites in the third exon of the bovine BMP4 gene
Authors: X. Zhong, L.S. Zan, H.B. Wang and Y.F. Liu
We examined the variation of the BMP4 gene in four Chinese indigenous cattle breeds and investigated the association of this polymorphism with body measurement traits. Using PCR-SSCP and DNA sequencing, a polymorphic microsatellite was detected in the third exon of the bovine BMP4 gene in 459 samples from four Chinese indigeno.. Read More»
- Genet. Mol. Res. 9(2):
- vol9-2gmr732
- DOI:
- 10.4238/vol9-2gmr732
Mining SNPs from EST sequences using filters and ensemble classifiers
Authors: J. Wang, Q. Zou and M.Z. Guo
Abundant single nucleotide polymorphisms (SNPs) provide the most complete information for genome-wide association studies. However, due to the bottleneck of manual discovery of putative SNPs and the inaccessibility of the original sequencing reads, it is essential to develop a more efficient and accurate computational method f.. Read More»
- Genet. Mol. Res. 9(2):
- vol9-2gmr765
- DOI:
- 10.4238/vol9-2gmr765
Genotoxic effects caused by indoor exposure to petroleum derivatives in a fuel quality control laboratory
Authors: A.E.O. Ara?ºjo, B.P. Mezzomo, ?. Ferrari and C.K. Grisolia
We looked for genotoxic effects in laboratory personnel routinely exposed to petroleum derivate compounds in an indoor environment. The exposed group of 21 workers from the Fuel Quality Control Laboratory of the Brazilian Petroleum Agency was matched with a group of 10 people from the staff of the Brazilian Ministry of Health... Read More»
- Genet. Mol. Res. 9(2):
- vol9-2gmr797
- DOI:
- 10.4238/vol9-2gmr797
Prediction of maize single-cross performance by mixed linear models with microsatellite marker information
Authors: M. Balestre, R.G. Von Pinho and J.C. Souza
We evaluated the potential of the best linear unbiased predictor (BLUP) along with the relationship coefficient for predicting the performance of untested maize single-cross hybrids. Ninety S0:2 progenies arising from three single-cross hybrids were used. The 90 progenies were genotyped with 25 microsatellite markers, with nin.. Read More»
- Genet. Mol. Res. 9(2):
- vol9-2gmr791
- DOI:
- 10.4238/vol9-2gmr791
A contact map matching approach to protein structure similarity analysis
Authors: Raquel C. de Melo, Carlos Eduardo R. Lopes, Fernando A. Fernandes Jr., Carlos Henrique da Silveira, Marcelo M. Santoro, Rodrigo L. Carceroni, Wagner Meira Jr.and Arnaldo de A. Ara?ºjo
We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-processing algorithms to measure t.. Read More»
- Genet. Mol. Res. 5(2):
PDB-Metrics: a Web tool for exploring the PDB contents
Authors: Renato Fileto, Paula R. Kuser, Michel E.B. Yamagishi, Andr?© A. Ribeiro, Thiago G. Quinalia, Eduardo H. Franco, Adauto L. Mancini, Roberto H. Higa, Stanley R.M. Oliveira, Edgard H. Santos, Fabio D. Vieira, Ivan Mazoni, Sergio A.B. Cruz and Goran Neshich
PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/ pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provid.. Read More»
- Genet. Mol. Res. 5(2):
Mining ORESTES no-match database: can we still contribute to cancer transcriptome?
Authors: Rog?©rio da Silva Fonseca, Dirce Maria Carraro and Helena Brentani
The Human Cancer Genome Project generated about 1 million expressed sequence tags by the ORESTES method, principally with the aim of obtaining data from cancer. Of this total, 341,680 showed no similarity with sequences in the public transcript databases, referred to as “no-match”. Some of them represent low abunda.. Read More»
- Genet. Mol. Res. 5(1):