Bioinformatics
Gene selection based on multi-class support vector machines and genetic algorithms
Authors: Bruno Feres de Souza and Andr�© Ponce de Leon F. de Carvalho
Microarrays are a new technology that allows biologists to better understand the interactions between diverse pathologic state at the gene level. However, the amount of data generated by these tools becomes problematic, even though data are supposed to be automatically analyzed (e.g., for diagnostic purposes). The issue become.. Read More»
- Genet. Mol. Res. 4(3):
A distributed computation of Interpro Pfam, PROSITE and ProDom for protein annotation
Authors: Edward de O. Ribeiro, Gustavo G. Zerlotini, Irving R.M. Lopes, Victor B.R. Ribeiro, Alba C.M. Melo, Maria Emilia M.T. Walter, Marcos Mota Costa and BIOFOCO Network
Interpro is a widely used tool for protein annotation in genome sequencing projects, demanding a large amount of computation and representing a huge time-consuming step. We present a strategy to execute programs using databases Pfam, PROSITE and ProDom of Interpro in a distributed environment using a Java-based messaging syste.. Read More»
- Genet. Mol. Res. 4(3):
Reconstruction of phylogenetic trees using the ant colony optimization paradigm
Authors: Mauricio Perretto and Heitor Silv�©rio Lopes
We developed a new approach for the reconstruction of phylogenetic trees using ant colony optimization metaheuristics. A tree is constructed using a fully connected graph and the problem is approached similarly to the well-known traveling salesman problem. This methodology was used to develop an algorithm for constructing a ph.. Read More»
- Genet. Mol. Res. 4(3):
An agent-based system for re-annotation of genomes
Authors: Leonardo Vianna do Nascimento and Ana L.C. Bazzan
Genome annotation projects can produce incorrect results if they are based on obsolete data or inappropriate models. We have developed an automatic re-annotation system that uses agents to perform repetitive tasks and reports the results to the user. These tasks involve BLAST searches on biological databases (GenBank) and the .. Read More»
- Genet. Mol. Res. 4(3):
An I/O device driver for bioinformatics tools: the case for BLAST
Authors: Renato Campos Mauro and S�©rgio Lifschitz
There are many bioinformatics tools that deal with input/ output (I/O) issues by using filing systems from the most common operating systems, such as Linux or MS Windows. However, as data volumes increase, there is a need for more efficient disk access, ad hoc memory management and specific page-replacement policies. We propos.. Read More»
- Genet. Mol. Res. 4(3):
Mutual information content of homologous DNA sequences
Authors: Helena Cristina G. Leit�£o, Luciana S. Pess�´a and Jorge Stolfi
The necessary information to reproduce and keep an organism is codified in acid nucleic molecules. Deepening the knowledge about how the information is stored in these bio-sequences can lead to more efficient methods of comparing genomic sequences. In the present study, we analyzed the quantity of information contained in a DN.. Read More»
- Genet. Mol. Res. 4(3):
Reconfigurable systems for sequence alignment and for general dynamic programming
Authors: Ricardo P. Jacobi, Mauricio Ayala-Rinc�³n, Luis G.A. Carvalho, Carlos H. Llanos and Reiner W. Hartenstein
Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic archi.. Read More»
- Genet. Mol. Res. 4(3):
A framework based on Web service orchestration for bioinformatics workflow management
Authors: Luciano A. Digiampietri, Claudia B. Medeiros and Jo�£o C. Setubal
Bioinformatics activities are growing all over the world, with proliferation of data and tools. This brings new challenges: how to understand and organize these resources and how to provide interoperability among tools to achieve a given goal. We defined and implemented a framework to help meet some of these challenges. Four i.. Read More»
- Genet. Mol. Res. 4(3):
Genomic cloning, expression, and single nucleotide polymorphism association analysis of the insulin-like androgenic gland hormone gene in the oriental river prawn (Macrobrachium nipponense)
Authors: F.J. Li, F.W. Jiang, H.K. Bai, H.T. Fu, S.B. Jin, S.M. Sun, H. Qiao and W.Y. Zhang
Increasing evidence suggests that the insulin-like androgenic gland hormone (IAG) gene plays an important role in male sexual differentiation, metabolism, and growth in crustaceans. In the present study, we isolated the full-length genome sequence of IAG by genome walking based on the cDNA sequence in Macrobrachium nipponense. Four novel single nucleotide.. Read More»
- Genet. Mol. Res. 14(2):
- 2015.June.1.8
- DOI:
- 10.4238/2015.June.1.8
Molecular cloning and tissue distribution of the Toll receptor in the black tiger shrimp, Penaeus monodon
Authors: W. Assavalapsakul and S. Panyim
The black tiger shrimp (Penaeus monodon) is economically important in many parts of the world, including Thailand. Shrimp immunity is similar to that of other invertebrate organisms; it consists of an innate immunity system. Toll or Toll-like receptors (TLRs) play an essential role in recognizing the cleaved form of the cytoki.. Read More»
- Genet. Mol. Res. 11(1):
- 2012.March.6.1
- DOI:
- 10.4238/2012.March.6.1