Bioinformatics
Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases
Authors: Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases
Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biologica.. Read More»
- Genet. Mol. Res. 6(4):
Genuine Bayesian multiallelic significance test for the Hardy-Weinberg equilibrium law
Authors: C.A.B. Pereira, F. Nakano, J.M. Stern and M.R. Whittle
Statistical tests that detect and measure deviation from the Hardy-Weinberg equilibrium (HWE) have been devised but are limited when testing for deviation at multiallelic DNA loci is attempted. Here we present the full Bayesian significance test (FBST) for the HWE. This test depends neither on asymptotic results nor on the num.. Read More»
- Genet. Mol. Res. 5(4):
Identification of a new Schistosoma mansoni membrane-bound protein through bioinformatic analysis
Authors: F.C. Cardoso, J.M.R. Pinho, V. Azevedo and S.C. Oliveira
Progress in schistosome genome research has enabled investigators to move rapidly from genome sequences to vaccine development. Proteins bound to the surface of parasites are potential vaccine candidates, or they can be used for diagnosis. We analyzed 4342 proteins deduced from the Schistosoma mansoni transcriptome with bioinf.. Read More»
- Genet. Mol. Res. 5(4):
Psychogenetics of Turner syndrome: an investigation of 28 subjects and respective controls using the Bender test and Piagetian scales
Authors: F.C.F. Ricardi, L.L. Zaia, I. Pellegrino-Rosa, J.T. Rosa, O.Z. Mantovani de Assis and P.H. Saldanha
Piagetian scales and the Bender visual motor gestalt test (BT) were applied to 28 subjects with universal 45,X Turner syndrome (TS), and their respective controls, in order to investigate their cognitive performance. Dermatoglyphics were also analyzed to obtain clues concerning embryological changes that may have appeared duri.. Read More»
- Genet. Mol. Res. 9(3):
- vol9-3gmr815
- DOI:
- 10.4238/vol9-3gmr815
Recognition of �±-helix transmembrane domains with an amphipathy scale generated by molecular dynamics using only the primary sequence of proteins
Authors: Mazze FM, Fuzo CA, Ciancaglini P and Degreve L
We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane.. Read More»
- Genet. Mol. Res. 6(2):
CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks
Authors: J. Schneider, F.-J. Vorh�¶lter, E. Trost, J. Blom, Y.R. Musa, H. Neuweger, K. Niehaus, S. Schatschneider, A. Tauch and A. Goesmann
New sequencing technologies provide ultra-fast access to novel microbial genome data. For their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction of metabolic networks is highly desirable. The software tool CARMEN performs in silico reconstruction of metabolic networks to interpret .. Read More»
- Genet. Mol. Res. 9(3):
- vol9-3gmr901
- DOI:
- 10.4238/vol9-3gmr901
The Star STING server: a multiplatform environment for protein structure analysis
Authors: G. Neshich, I. Mazoni, S.R.M. Oliveira, M.E.B. Yamagishi, P.R. Kuser-Falc�£o, L.C. Borro, D.U. Morita, K.R.R. Souza, G.V. Almeida, D.N. Rodrigues, J.G. Jardine, R.C. Togawa, A.L. Mancini, R.H. Higa, S.A.B. Cruz, F.D. Vieira, E.H. Santos, R.C. Melo and M.M. Santoro
Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB.. Read More»
- Genet. Mol. Res. 5(4):
Personalized diagnosis by cached solutions with hypertension as a study model
Authors: P.C. Carvalho, S.S. Freitas, A.B. Lima, M. Barros, I. Bittencourt, W. Degrave, I. Cordovil, R. Fonseca, M.G.C. Carvalho, R.S. Moura Neto and P.H. Cabello
Statistical modeling of links between genetic profiles with environmental and clinical data to aid in medical diagnosis is a challenge. Here, we present a computational approach for rapidly selecting important clinical data to assist in medical decisions based on personalized genetic profiles. What could take hours or days of .. Read More»
- Genet. Mol. Res. 5(4):
Splice site prediction using stochastic regular grammars
Authors: Kashiwabara AY, Vieira DCG, Machado-Lima A and Durham AM
This paper presents a novel approach to the problem of splice site prediction, by applying stochastic grammar inference. We used four grammar inference algorithms to infer 1465 grammars, and used 10-fold cross-validation to select the best grammar for each algorithm. The corresponding grammars were embedded into a classifier a.. Read More»
- Genet. Mol. Res. 6(1):
An improved K-means clustering method for cDNA microarray image segmentation
Authors: T.N. Wang, T.J. Li, G.F. Shao and S.X. Wu
Microarray technology is a powerful tool for human genetic research and other biomedical applications. Numerous improvements to the standard K-means algorithm have been carried out to complete the image segmentation step. However, most of the previous studies classify the image into two clusters. In this paper, we propose a novel K-means algorithm, which .. Read More»
- Genet. Mol. Res. 14(3):
- 2015.July.14.3
- DOI:
- 10.4238/2015.July.14.3