The Staden Package, 1998

Staden, Rodger; Beal, Kathryn F.; Bonfield, James K.

doi:10.1385/1-59259-192-2:115

Cited by 949 publications

(855 citation statements)

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“…IST chromatogram files, in Applied Biosystems INC (ABI) or Standard Chromatogram Format (SCF) formats, are filtered by Phred-pregap4 software (20) to extract nucleic sequences and their associated quality values. The resulting nucleic sequence of each IST is then translated into three frames and aligned against a protein sequence database (as defined in the configuration file by users, typically Ensembl or NCBI databases) by using BLASTX alignment software (21).…”

Section: Grow Each Yeast Bait Colony Overnight In 2 ML Sd-w Under Agimentioning

confidence: 99%

Virus–Human Cell Interactomes

Tafforeau¹,

Rabourdin–Combe²,

Lotteau³

2011

Methods in Molecular Biology

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Using global approaches and high-throughput technologies in virology brings a new vision of the infections physiology and allows the identification of cellular factors, mandatory for viral life cycle, that could be targeted by original therapeutic agents. It opens perspectives for the treatment of viral infections by acting on cellular pathways that the virus must use for its own replication. Combining these new molecules with classical antiviral drugs and immunomodulators diversifies and enlarges the antiviral arsenal and contributes to fight drug resistance.Our laboratory and others are constructing virus-human interactomes to propose a comprehensive analysis of viral infection at the cellular level. Studying these infection maps, where the viral infection can be visualized as perturbation of the human protein-protein interaction network, and identifying the biological functions that are impaired by these perturbations may lead to discovery of new therapeutic targets. These virus-human interaction maps are constructed in a stringent yeast two-hybrid system by screening human cDNA libraries with viral proteins as bait and integrating interactions mined from literature and public databases. Key words:Yeast two-hybrid screen, Mating, Yeast two-hybrid array, Protein-protein interactionThe rapidly growing knowledge of protein-protein interaction networks (interactomes) for model organisms and human provides a network-based model to understand molecular and cellular biology. Recently, virus-host relationships also began to be studied at the proteome level by identifying interactions between viral and host-cell proteins (1-5), as reviewed in ref. 6. These virus-host interactomes compose a repertoire of interactions between viral and human proteins that can be analyzed in a network approach. By this mean, viral infections can be viewed as the expression of new constraints imposed by the virus on the cellular interactome.

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Section: Grow Each Yeast Bait Colony Overnight In 2 ML Sd-w Under Agimentioning

confidence: 99%

Virus–Human Cell Interactomes

Tafforeau¹,

Rabourdin–Combe²,

Lotteau³

2011

Methods in Molecular Biology

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“…The quality assessment of the nucleotide sequences and the contig assembly were carried out using the Staden Package (Staden et al, 1998). Multiple sequence alignments of each gene were determined using ClustalW as implemented in MEGA v.5 (Tamura et al, 2011) and were manually adjusted to allow maximum sequence similarity.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Polyphasic analysis of Acidovorax citrulli strains from northeastern Brazil

Silva

Xavier

Gama

et al. 2016

Sci. agric. (Piracicaba, Braz.)

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Bacterial fruit blotch (BFB) of cucurbit plants is caused by Acidovorax citrulli and represents a serious concern to melon (Cucumis melo L.) growers worldwide, including those in Brazil. Thirty-four A. citrulli strains from different melon production areas of northeastern Brazil were characterized for their virulence on melon fruits and their substrate utilization and molecular profiles. Based on the analysis of BFB severity on melon fruits, the A. citrulli strains were divided into three groups, classified as mildly, moderately or highly virulent. Although host-related groups were not observed, the watermelon and 'melão-pepino' strains exhibited only low or moderate virulence on melon fruit. Substrate utilization profiles revealed that 94 % of the 95 tested compounds were used by A. citrulli strains as a carbon source. Overall, based on substrate utilization, low variability was observed with no relationship to host of origin. The formation of one group of A. citrulli strains based on Repetitive Sequence-based PCR (rep-PCR) analysis confirmed the low variability observed in the substrate utilization analyses. Bayesian inference based on the analysis of 23S rDNA partial sequence data resulted in one well-supported clade and clustered the strains with the A. citrulli-type species with high posterior probability support. Based on the markers used, the Brazilian A. citrulli strains belong to a single group, which corresponds to the previously described Group I for this bacterium in the United States.

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“…PCR product was sequenced by ACT Gene Análises Moleculares (Centro de Biotecnologia, UFRGS, Brazil) using the automatic sequencer ABI-PRISM 3100 genetic analyzer (Applied Biosystems). Chromatograms obtained by sequencing were analyzed, and consensus sequences were assembled using 4 sStaden package programs (STADEN et al, 2000).…”

Section: Este Relato Descreve Os Achados Clínicos Patológicos E Micrmentioning

confidence: 99%