bioprotocols

Mfold web server for nucleic acid folding and hybridization prediction

Posted on by Oscar

Mfold web server for nucleic acid folding and hybridization prediction

The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software.
Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’.

bioprotocols

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase

A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

Molecular portraits of human breast tumours

Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell’s identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour.
Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns.

Studies on transformation of Escherichia coli with plasmids

Factors that affect the probability of genetic transformation of Escherichia coli by plasmids have been evaluated. A set of conditions is described under which about one in every 400 plasmid molecules produces a transformed cell. These conditions include cell growth in medium containing elevated levels of Mg2+, and incubation of the cells at 0 degrees C in a solution of Mn2+, Ca2+, Rb+ or K+, dimethyl sulfoxide, dithiothreitol, and hexamine cobalt (III). Transformation efficiency declines linearly with increasing plasmid size. Relaxed and supercoiled plasmids transform with similar probabilities.
Non-transforming DNAs compete consistent with mass. No significant variation is observed between competing DNAs of different source, complexity, length or form. Competition with both transforming and non-transforming plasmids indicates that each cell is capable of taking up many DNA molecules, and that the establishment of a transformation event is neither helped nor hindered significantly by the presence of multiple plasmids.

PAML 4: phylogenetic analysis by maximum likelihood

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations.
This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at — (http://abacus.gene.ucl.ac.uk/software/paml.html).

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Description: Anti-Flag magnetic beads is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody. It is recommended to use for co-immunoprecipitation and protein purification.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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EUR 254.4
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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EUR 1668
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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EUR 1668
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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EUR 261.6
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Amino Magnetic Particles
AM-40-100 100 mL
EUR 1668
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Amino Magnetic Particles
AM-60-10 10 mL
EUR 376.8
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Amino Magnetic Particles
AM-60-100 100 mL
EUR 2593.2
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Amino Magnetic Particles
AM-80-10 10 mL
EUR 444
Description: Amino Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

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EUR 267.6
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

Epoxy Magnetic Particles
EM-20-10 10 mL
EUR 267.6
Description: Epoxy Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Epoxy Magnetic Particles
EM-20-100 100 mL
EUR 1716
Description: Epoxy Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Magnetic Separation Rack
M1501-1 1 Rack
EUR 454.8

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CM101 32 well (200 μl/well)
EUR 112

Magnetic Separation Rack
CM103 24 well (1.5 ml/well)
EUR 112

GFP-nAb Magnetic 0.5ml
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RFP-nAb Magnetic 0.5ml
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Biotin Magnetic Particles
TM-10-10 10 mL
EUR 254.4
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

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TM-40-10 10 mL
EUR 254.4
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

Biotin Magnetic Particles
TM-60-5 5 mL
EUR 426
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

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TMX-10-10 10 mL
EUR 273.6
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

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EUR 315.6
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VM-40-10 10 mL
EUR 315.6
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VM-60-10 10 mL
EUR 388.8
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VM-80-5 5 mL
EUR 438
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

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VMS-30-10 10 mL
EUR 346.8
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Avidin Magnetic Particles
VMS-40-10 10 mL
EUR 346.8
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

Avidin Magnetic Particles
VMX-10-10 10 mL
EUR 261.6
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

Avidin Magnetic Particles
VMX-40-5 5 mL
EUR 315.6
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

GFP-nAb Magnetic 0.25ml
ABP-NAB-GFPM025 250 µl Ask for price

RFP-nAb Magnetic 0.25ml
ABP-NAB-RFPM025 250 µl Ask for price

nAb Magnetic Control 0.5ml
ABP-NAB-MCNTRL5 500 µl Ask for price

Carboxyl Magnetic Particles
CM-025-10 10 mL
EUR 249.6
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Carboxyl Magnetic Particles
CM-025-100H 100mL
EUR 1765.2
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Carboxyl Magnetic Particles
CM-025-10H 10mL
EUR 237.6
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Carboxyl Magnetic Particles
CM-05-10 10 mL
EUR 249.6
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Carboxyl Magnetic Particles
CM-05-10H 10mL
EUR 249.6
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Carboxyl Magnetic Particles
CM-08-10 10 mL
EUR 249.6
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.

Carboxyl Magnetic Particles
CM-10-10 10 mL
EUR 254.4
Description: Carboxyl Magnetic Particles are prepared by coating a layer of magnetite and polystyrene onto monodispersed (i.e.. uniform sized) polystyrene core particles. The magnetic particles can be easily separated from a suspension magnetically. These particles become non magnetic when removed from a magnet, and do not retain any detectable magnetism even after repeated exposure to strong magnetic field.Are of research that those particles had been tested are cell separation, affinity purification, DNA probe assays, magnetic particle EIA. For more infomation please don't hesiate to contact our technical team.