Bioinformatics
Genome sequence compression based on optimized context weighting
Authors: M. Chen, J.J. Shao and X.M. Jia
Context weighting is an important technology for genome compression. In this study, we discuss the relationship between the weighting of context models and the weighting of the description lengths corresponding to their respective context models. It indicates that weighting of context models is equivalent to the weighting of t.. Read More»
- Genet. Mol. Res. 16(2):
- gmr16026784
- DOI:
- 10.4238/gmr16026784
Association of interleukin-1�² -511C/T promoter polymorphism with COPD risk: a meta-analysis
Authors: Y.S. Wang, L. Liu, X.Y. Xu, J.L. Wang, H. Zhou, T.L. Li and Z.A. Liang
Studies examining the role of interleukin (IL)-1β -511C/ T promoter polymorphism in the pathogenesis of chronic obstructive pulmonary disease (COPD) have shown inconsistent results. This metaanalysis was performed to assess the association between the IL-1β -511C/T promoter polymorphism and COPD susceptibility. Published case-control, cross-sect.. Read More»
- Genet. Mol. Res. 14(2):
- 2015.May.4.5
- DOI:
- 10.4238/2015.May.4.5
Taxonomic status of Pinus henryi using multiplexed microsatellite markers
Authors: Q. Xie, Z.-H. Liu and Z.-Q. Li
The taxonomic status of Pinus henryi, a rare species endemic to China, is still ambiguous. In this study, the genetic relationships among P. henryi and its congeners (P. tabulaeformis, P. tabulaeformis var. mukdensis, and P. massoniana) were revealed using multiplexed microsatellite markers, including chloroplast microsatellites, nuclear microsatellites, .. Read More»
- Genet. Mol. Res. 14(2):
- 2015.May.4.13
- DOI:
- 10.4238/2015.May.4.13
Application of latent semantic indexing to evaluate the similarity of sets of sequences without multiple alignments character-by-character
Authors: Couto BRGM, Ladeira AP and Santos MA
Most molecular analyses, including phylogenetic inference, are based on sequence alignments. We present an algorithm that estimates relatedness between biomolecules without the requirement of sequence alignment by using a protein frequency matrix that is reduced by singular value decomposition (SVD), in a latent semanrelattic .. Read More»
- Genet. Mol. Res. 6(4):
A simple genetic algorithm for multiple sequence alignment
Authors: Gondro C and Kinghorn BP
Multiple sequence alignment plays an important role in molecular sequence analysis. An alignment is the arrangement of two (pairwise alignment) or more (multiple alignment) sequences of ‘residues’ (nucleotides or amino acids) that maximizes the similarities between them. Algorithmically, the problem consists of ope.. Read More»
- Genet. Mol. Res. 6(4):
Finding protein-protein interaction patterns by contact map matching
Authors: Melo RC, Ribeiro C, Murray CS, Veloso CJM, da Silveira CH, Neshich G, Meira Jr. W, Carceroni RL and Santoro MM
We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can com.. Read More»
- Genet. Mol. Res. 6(4):
BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database
Authors: Faria-Campos AC, Gomes RR, Moratelli FS, Rausch-Fernandes H, Franco GR and Campos SVA
Proteomics correspond to the identification and quantitative analysis of proteins expressed in different conditions or life stages of a cell or organism. Methods used in proteomics analysis include mainly chromatography, two-dimensional electrophoresis and mass spectrometry. Data generated in proteomics analysis vary significa.. Read More»
- Genet. Mol. Res. 6(4):
Electrostatic potential calculation for biomolecules - creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures
Authors: Rocchia W and Neshich G
STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes u.. Read More»
- Genet. Mol. Res. 6(4):
Sting_rdb: a relational database of structural parameters for protein analysis with support for data warehousing and data mining
Authors: Oliveira SRM, Almeida GV, Souza KRR, Rodrigues DN, Kuser-Falcao PR, Yamagishi MEB, Santos EH, Vieira FD, Jardine JG and Neshich G
An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one’s ability to better handle scientific objectives and interpret the research results. To ach.. Read More»
- Genet. Mol. Res. 6(4):
Ab initio 3-D structure prediction of an artificially designed three-�±-helix bundle via all-atom molecular dynamics simulations
Authors: Breda A, Santos DS, Basso LA and Norberto de Souza O
The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the c.. Read More»
- Genet. Mol. Res. 6(4):