PlasMapper: a web server for drawing and auto-annotating plasmid maps

Dong, Xiaoli; Stothard, Paul; Forsythe, Ian J.; Wishart, David S.

doi:10.1093/nar/gkh410

Cited by 71 publications

(54 citation statements)

References 10 publications

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“…The sequence of the pRAP15 vector used in the study was determined prior to the analysis (Eurofins MWG Operon, Huntsville, Alabama; Matsye et al 2012). From that sequence information, the vector map for pRAP15 was made by taking its confirmed sequence information and entering it into PlasMapper Version 2.0 (Dong et al 2004). The pRAP15 vector has a single Gateway® (Invitrogen®)-compatible attR1-ccdB-attR2 cassette.…”

Section: Prap15 Plasmidmentioning

confidence: 99%

A plant transformation system designed for high throughput genomics inGossypium hirsutumto study root–organism interactions

Pant

McNeece

Sharma

et al. 2015

Journal of Plant Interactions

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The study of biological processes has been aided greatly by the development of procedures to identify the large numbers of associated genes. However, the ability to study the identified genes experimentally is often impeded by the absence of technologies to perform such functional analyses. Here, a nonaxenic plant transformation system has been developed in Gossypium hirsutum (cotton) for the study of genes associated with root functions and root-organism interactions. The plant transformation system is compatible with modern high throughput plant transformation goals and the processing of large numbers of genes intended for the study of root function in G. hirsutum.

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Section: Prap15 Plasmidmentioning

confidence: 99%

A plant transformation system designed for high throughput genomics inGossypium hirsutumto study root–organism interactions

Pant

McNeece

Sharma

et al. 2015

Journal of Plant Interactions

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“…( A ) Plasmid map of the yeast surface display vector pCT302 with a single-chain T cell receptor (scTCR) cloned in as a fusion with the yeast mating agglutinin protein Aga-2. Map was prepared with the help of PlasMapper (48). The open reading frame containing Aga-2 and the scTCR is expanded to show the important elements and restriction sites.…”

Section: Figmentioning

confidence: 99%

Biosensor Detection Systems: Engineering Stable, High-Affinity Bioreceptors by Yeast Surface Display

Richman

Kranz

Stone

2009

Biosensors and Biodetection

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Over the past two decades, the field of biosensors has been developing fast, portable, and convenient detection tools for various molecules of interest, both biological and environmental. While much attention is paid to the transduction portion of the sensor, the actual bioreceptor that binds the ligand is equally critical. Tight, specific binding by the bioreceptor is required to detect low levels of the relevant ligand, and the bioreceptor must be stable enough to survive immobilization, storage, and in ideal cases, regeneration on the biosensing device. Often, naturally-occurring bioreceptors or antibodies that are specific for a ligand either express affinities which may be too low to detect useful levels, or the proteins are too unstable to be used and re-used as a biosensor. Further engineering of these receptors can improve their utility. Here, we describe in detail the use of yeast surface display techniques to carry out directed evolution of bioreceptors to increase both the stability of the molecules and their affinity for the ligands. This powerful technique has enabled the production of stabilized, single-chain antibodies, T cell receptors, and other binding molecules that exhibit affinity increases for their ligands of up to 1 million-fold and expression of stable molecules in E. coli.

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“…Obtained scaffolds were assembled to full-length mitogenome and closed to circular mtDNA. The mitogenome was annotated using PlusMapper (Dong et al 2004) and was manually adjusted. ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) was used to verify annotated genes and to identify any potential genes in uncoding regions.…”

mentioning

confidence: 99%

The complete mitogenome of Mycosphaerella pinodes (Ascomycota, Mycosphaerellaceae)

Okorski

Pszczółkowska

Jastrzebski

et al. 2016

Mitochondrial DNA Part B

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In this study, the complete mitochondrial genome of plant pathogenic fungus, Mycosphaerella pinodes , was sequenced. The nucleotide composition of the genome is: 36.0% of A, 15.0% of C, 14.6% of G and 34.5% of T. The mitochondrial genome is 55 973 bp in length and consists of 11 protein-coding genes, two ribosomal RNAs and 25 tRNA genes. The mitogenome analysis of M . pinodes provide a molecular basis for further studies on molecular systematics and evolutionary dynamics of Ascomycetes fungi especially belonging to Dothideomycetes.

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PlasMapper: a web server for drawing and auto-annotating plasmid maps

Cited by 71 publications

References 10 publications

A plant transformation system designed for high throughput genomics inGossypium hirsutumto study root–organism interactions

A plant transformation system designed for high throughput genomics inGossypium hirsutumto study root–organism interactions

Biosensor Detection Systems: Engineering Stable, High-Affinity Bioreceptors by Yeast Surface Display

The complete mitogenome of Mycosphaerella pinodes (Ascomycota, Mycosphaerellaceae)

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