Research Article

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09/30/2005
Agent-based systems; Bioinformatics; Re-annotation

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 use of detection tools (Genemark and Glimmer) to identify ... more

L.Vianna do Nascimento; A.L.C. Bazzan
09/30/2005
Bioinformatics; Semantic web; Web service; Workflow

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 issues were considered: the use of Web services as a basic ... more

L.A. Digiampietri; C.B. Medeiros; J.C. Setubal
08/26/2011
2-D gel electrophoresis; Bartonella henselae; Bioinformatics; MS; Outer membrane protein

Bartonella henselae, an infectious agent causing cat-scratch disease and vasculoproliferative disorders in humans, is a fastidious facultative intracellular pathogen. The outer membrane proteins of B. henselae are key molecules that play a primary role in host-cell interactions. We isolated B. henselae outer membrane proteins, using the ionic detergent N-lauroyl ... more

D.M. Li; Q.Y. Liu; F. Zhao; Y. Hu; D. Xiao; Y.X. Gu; X.P. Song; J.Z. Zhang
06/17/2014
Bioinformatics; Duck plague virus; Function; Glycoprotein C; Structure

Glycoprotein C is one of the duck plague virus (DPV) glycoproteins and is encoded by the DPV UL44 gene. DPV glycoprotein C (DPV-gC) comprises 431 amino acids with a putative molecular mass of 47.35 kDa. Sequence analysis indicated that the protein possesses typical characteristics of type-I membrane glycoproteins, containing an N-terminal signal sequence, an external domain, a C-terminal ... more

K.F. Sun; A.C. Cheng; M.S. Wang
03/31/2006
Expressed sequence tag; Sequence trimming; Slippage; Sugar cane

Slippage is an important sequencing problem that can occur in EST projects. However, very few studies have addressed this. We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291,689 EST ... more

C. Baudet; Z. Dias
06/29/2005
Expressed sequence tag; Paracoccidioides brasiliensis; RNA modifications; Splicing; Transcription; Transcriptome analysis

The RNA biogenesis machinery of Paracoccidioides brasiliensis was assessed by comparative analyses of PbAESTs (P. brasiliensis assembled expressed sequence tags (ESTs)) with sequences from Saccharomyces cerevisiae MIPS database. PbAESTs related to almost all categories of S. cerevisiae RNA biogenesis were found. Two of the 12 S. cerevisiae ... more

P. Albuquerque; A.J. Baptista; Lda Silveir Derengowsky; L. Procópio; A.Moraes Nicola; F.B.M. Arraes; D.Paulo de Souza; C.Maria Kyaw; I. Silva-Pereira
08/25/2009
Bovine; Contig; Cluster; Expressed sequence tag; Gene atlas; Transcriptional profiling

Genes whose products function in a common biological process are often co-regulated. When regulation occurs at the transcriptional level, co-expressed genes can be detected globally by expression arrays or by sequencing non-normalized cDNA libraries. We examined bovine gene expression in 27 tissues using non-normalized cDNA library sequencing. Contigs were generated from expressed ... more

O.M. Keane; N. Maqbool; A.F. McCulloch; J.C. McEwan; K.G. Dodds
11/02/2008
Biological control; Differential display reverse transcriptase; Expressed sequence tag; Nematophagous; Single nucleotide polymorphisms

The technology of mRNA-based differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR) was used to detect a 246-bp differentially expressed fragment from the nematophagous fungus Arthrobotrys oviformis when young mycelia were induced with the round worm Haemonchus contortus. The fragment was converted into an expressed sequence tag (EST) through ... more

A. Nagee; A. Acharya; A. Shete; P.N. Mukhopadhyaya; B.A. Aich
05/04/2010
Ensemble classifier; Expressed sequence tag; Filter; Singlenucleotide polymorphisms; SNPDigger

Abundant single nucleotide polymorphisms (SNPs) provide the most complete information for genome-wide association studies. However, due to the bottleneck of manual discovery of putative SNPs and the inaccessibility of the original sequencing reads, it is essential to develop a more efficient and accurate computational method for automated SNP detection. We propose a novel computational ... more

J. Wang; Q. Zou; M.Z. Guo
06/11/2010
Bamboo; Expressed sequence tag; Flowering; Mechanism

Unlike other plants, bamboo (Bambusoideae) flowering is an elusive physiological phenomena, because it is unpredictable, long-periodic, gregarious, and uncontrollable; also, bamboo plants usually die after flowering. The flowering mechanism in Arabidopsis thaliana, a eudicot model species, is well established, but it remains unknown in bamboo species. We found 4470 and 3878 ... more

X.C. Lin; T.Y. Chow; H.H. Chen; C.C. Liu; S.J. Chou; B.L. Huang; C.I. Kuo; C.K. Wen; L.C. Huang; W. Fang

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