Related GMR Articles

Bioinformatics; Genetic determinism; Genomics; Human genome; Public understand of science; Science and technology studies

The literature about genomics and bioinformatics achievements in high-impact journals such as Nature and Science has raised disproportionate expectations amongst the general public about fast and revolutionary drugs and breakthroughs in biomedicine. However, the yield obtained by database mining activities has been modest, as reported in the February 2001 issues of ... more

M. Leite
Alternative splicing; Bioinformatics; Exon skipping; Expressed sequences; Extracellular matrix; Human transcriptome

Alternative splicing increases protein diversity through the generation of different mRNA molecules from the same gene. Although alternative splicing seems to be a widespread phenomenon in the human transcriptome, it is possible that different subgroups of genes present different patterns, related to their biological roles. Analysis of a subgroup may enhance common features of its ... more

N.Jo Sakabe; M.Dulcetti Vibranovski; S.José de Souza
Bioinformatics; DNA sequence analysis software; Perl programming

A lack of pliant software tools that support small- to medium-scale DNA sequencing efforts is a major hindrance for recording and using laboratory workflow information to monitor the overall quality of data production. Here we describe VSQual, a set of Perl programs intended to provide simple and powerful tools to check several quality features of the sequencing data generated by ... more

E. Binneck; J.Flávio V. Silva; N. Neumaier; J.Renato B. Farias; A.L. Nepomuceno
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
Bioinformatics; Latent semantic indexing; Molecular comparisons; Sequence alignments

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 semantic index information retrieval system. Two databases were used: one ... more

B.R.G.M. Couto; A.P. Ladeira; M.A. Santos
Bioinformatics; Flagellar motility; Genome screens; Intraflagellar transport; Intraflagellar transport complex; Leishmania

Flagella are constructed and maintained through the highly conserved process of intraflagellar transport (IFT), which is a rapid movement of particles along the axonemal microtubules of cilia/flagella. Particles that are transported by IFT are composed of several protein subunits comprising two complexes (A and B), which are conserved among green algae, nematodes, and vertebrates. To ... more

J.J.S. Gouveia; E.J.R. Vasconcelos; A.C.L. Pacheco; R. Araújo-Filho; A.R.S. Maia; M.T. Kamimura; M.P. Costa; D.A. Viana; R.B. Costa; R. Maggioni; D.M. Oliveira
Bioinformatics; Membrane-bound protein; Schistosoma mansoni; Sm29; Transcriptome; Vaccine

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 bioinformatic computer programs. Thirty-four proteins had ... more

F.C. Cardoso; J.M.R. Pinho; V. Azevedo; S.C. Oliveira
Apis mellifera; Bioinformatics; doublesex gene; Evolution of genes; Molecular genetics; Sex determination; Sexual development; Transcription factors

A comparison of the most conserved sex-determining genes between the fruit fly, Drosophila melanogaster, and the honey bee, Apis mellifera, was performed with bioinformatics tools developed for computational molecular biology. An initial set of protein sequences already described in the fruit fly as participants of the sex-determining cascade was retrieved from the Gene ... more

A.S. Cristino; A.Mendes do Nascimento; Lda Fontour Costa; Z.Luz Paulin Simões
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