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Bioinformatics; Biotechnology; Brazil; Genomics; Microbial genome project; Prokaryotes

Since the Haemophilus influenzae genome sequence was completed in 1995, 172 other prokaryotic genomes have been completely sequenced, while 508 projects are underway. Besides pathogens, organisms important in several other fields, such as biotechnology and bioremediation, have also been sequenced. Institutions choose the organisms they wish to sequence according to the ... more

P.Borges San Celestino; L.Rodrigues de Carvalho; L.Martins de Freitas; N.Florêncio Martins; L.Gustavo Ca Pacheco; A. Miyoshi; V. Azevedo; F.Alves Dorella
Bioinformatics; Brain; GPCR; Orphan receptor; Prostate cancer; Testis

G protein-coupled receptors (GPCRs) are involved in a large variety of physiological functions. The number of known members that belong to this large family of receptors has been rapidly increasing. Now, with the availability of the human genome sequence databases, further family members are being identified. We describe the identification of a novel GPCR that shows no significant ... more

R.B. Parmigiani; G.S. Magalhães; P.A.F. Galante; C.V.B. Manzini; A.A. Camargo; B. Malnic
Bayesian bootstrap; Bioinformatics; Gene expression; Microarray; Statistics; Web tool

One of the goals of gene expression experiments is the identification of differentially expressed genes among populations that could be used as markers. For this purpose, we implemented a model-free Bayesian approach in a user-friendly and freely available web-based tool called BayBoots. In spite of a common misunderstanding that Bayesian and model-free approaches are incompatible, ... more

R.Z.N. Vêncio; D.F.C. Patrão; C.S. Baptista; C.A.B. Pereira; B. Zingales
Bioinformatics; Gene expression analysis; Machine learning; Novelty detection; Support vector machines

Novelty detection techniques might be a promising way of dealing with high-dimensional classification problems in Bioinformatics. We present preliminary results of the use of a one-class support vector machine approach to detect novel classes in two Bioinformatics databases. The results are compatible with theory and inspire further investigation.

E.J. Spinosa; A.C.P.L.F. de Carvalho
Bioinformatics; Cancer; Expressed sequence tags; Gene discovery; ORESTES

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 abundance or difficult to detect human transcripts, but part of these ... more

Rda Silva Fonseca; D.Maria Carraro; H. Brentani
Ant colony optimization; Bioinformatics; Evolutionary computation; Phylogeny

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 phylogenetic tree using a pheromone matrix. Two data sets ... more

M. Perretto; H.Silvério Lopes
Automatic annotation; Bioinformatics; Differential transcriptome; Expressed sequence tags; Paracoccidioides brasiliensis

Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an endemic mycosis of Latin America. This fungus presents a dimorphic character; it grows as a mycelium at room temperature, but it is isolated as yeast from infected individuals. It is believed that the transition from mycelium to yeast is important for the infective process. The Functional ... more

M.M. Brígido; M.Emilia M.T. Walter; M.Emilia M.T. Walter; A.G. Oliveira; M.K. Inoue; D.S. Anjos; E.F.O. Sandes; J.J. Gondim; M.José de A. Carvalho; N.F. Almeida; M.Sueli Soar Felipe
Bioinformatics; Expressed sequence tags; Single nucleotide polymorphisms; Witches’ broom disease

In order to increase the efficiency of cacao tree resistance to witches’ broom disease, which is caused by Moniliophthora perniciosa (Tricholomataceae), we looked for molecular markers that could help in the selection of resistant cacao genotypes. Among the different markers useful for developing marker-assisted selection, single nucleotide polymorphisms (SNPs) constitute the ... more

L.S. Lima; K.P. Gramacho; N. Carels; R. Novais; F.A. Gaiotto; U.V. Lopes; A.S. Gesteira; H.A. Zaidan; J.C.M. Cascardo; J.L. Pires; F. Micheli
Bioinformatics; Genetic variability; Pattern recognition; Quasispecies

The results obtained through biological research usually need to be analyzed using computational tools, since manual analysis becomes unfeasible due to the complexity and size of these results. For instance, the study of quasispecies frequently demands the analysis of several, very lengthy sequences of nucleotides and amino acids. Therefore, bioinformatics tools for the study of quasispecies ... more

E.A. Marucci; G.F.D. Zafalon; A.C.G. Jardim; L.H.T. Yamasaki; C. Bittar; P. Rahal; J.M. Machado
Bioinformatics; Caffeine synthase; Full-length cDNA; Guarana; Transcriptome

The current intense production of biological data, generated by sequencing techniques, has created an ever-growing volume of unanalyzed data. We reevaluated data produced by the guarana (Paullinia cupana) transcriptome sequencing project to identify cDNA clones with complete coding sequences (full-length clones) and complete sequences of genes of biotechnological interest, ... more

L.C. Figueirêdo; A.C. Faria-Campos; S. Astolfi-Filho; J.L. Azevedo