Research Article

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Alternative splicing; SAGE; Tumorigenesis

Although alternative splicing of many genes has been found associated with different stages of tumorigenesis and splicing variants have been characterized as tumor markers, it is still not known whether these examples are sporadic or whether there is a broader association between the two phenomena. In this report we evaluated, through a bioinformatics approach, the expression of ... more

N. Kirschbaum-Slager; G.M.P. Lopes; P.A.F. Galante; G.J. Riggins; S.J. de Souza
astrocytomas; COL6A1 gene; differential gene expression; SAGE; tumor marker

Diffuse infiltrating gliomas are the most common tumors of the central nervous system. Gliomas are classified by the WHO according to their histopathological and clinical characteristics into four classes: grade I (pilocytic astrocytoma), grade II (diffuse astrocytoma), grade III (anaplastic astrocytoma), and grade IV (glioblastoma multiforme). Several genes have already been correlated with ... more

A. Fujita; J.R. Sato; F. Festa; L.R. Gomes; S.M. Oba-Shinjo; S.K.N. Marie; C.E. Ferreira; M.C. Sogayar
Amoebae; Dictyostelium discoideum; SAGE; Transcriptome

The unusual life cycle of Dictyostelium discoideum, in which an extra-cellular stressor such as starvation induces the development of a multicellular fruiting body consisting of stalk cells and spores from a culture of identical amoebae, provides an excellent model for investigating the molecular control of differentiation and the transition from single- to multi-cellular life, ... more

T.J. Whitney; D.G. Gardner; M.L. Mott; M. Brandon
Assembling; CAP3; Codifying sequences; Consensus; PHRED; Sequencing reads; Trimming

The production of nucleic acid sequences by automatic DNA sequencer machines is always associated with some base-calling errors. In order to produce a high-quality DNA sequence from a molecule of interest, researchers normally sequence the same sample many times. Considering base-calling errors as rare events, re-sequencing the same molecule and assembling the reads produced are ... more

F. Prosdocimi; D.A.O. Lopes; F.C. Peixoto; M.M. Mourão; L.G.G. Pacífico; R.A. Ribeiro; J.M. Ortega
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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 propose a device driver that can be used by multiple ... more

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Annotation; BLAST; Expressed sequence tags; KEGG Orthology; orthologs

The KEGG Orthology (KO) database was tested as a source for automated annotation of expressed sequence tags (ESTs). We used a control experiment where every EST was assigned to its cognate protein, and an annotation experiment where the ESTs were annotated by proteins from other organisms. Analyzing the results, we could assign classes to the annotation: correct, changed and speculated. The ... more

G.R. Fernandes; M.A. Mudado; J.M. Ortega
BLAST; Conservation measures; nrDNA; Rare species

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA ... more

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BLAST; Blast resistance; QTL mapping; Recombinant inbred lines; Rice

Bodao, a japonica landrace from the Taihu Lake region of China, is highly resistant to most Chinese isolates of Magnaporthe oryzea, a form of rice blast. To effectively dissect the influence of genetics on this blast resistance, a population of 155 recombinant inbred lines (F2:8) derived from a cross of Bodao x Suyunuo was inoculated with 12 blast isolates. ... more

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BLAST; Chloroplast loci; DNA barcoding; Nuclear DNA marker

Genuine medicinal plant materials are very important for potential crude drug production, which can be used to cure many human diseases. DNA barcoding of medicinal plants is an effective way to identify adulterated or contaminated market materials, but it can be quite challenging to generate barcodes and analyze the data to determine discrimination power. The molecular phylogeny of a ... more

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Anacardium occidentale; BLAST; Cashew; DNA fingerprinting; ITS region; PCR; extraction DNA

This study performed a genetic study of several canopies of Anacardium occidentale L. specimen called "Cashew King" (Cajueiro da Praia-PI, Brazil) in order to assess whether all canopies belong to the same plant. Leaves were collected from  different distant points, and preserved for analysis of DNA. The analysis was made from automated sequencing by capillary ... more

F.P.M. do Amaral; G.H. de Sa; L.A. Filgueiras; F.S.Santos Filho; C.J.R.Santos Soares; M.P.M. do Amaral; S.E. dos Sant Valente; A.N. Mendes