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).

DNA Purification SPRI Magnetic Beads (5 ml)
G950 5 ml
EUR 115

DNA Purification SPRI Magnetic Beads (25 ml)
G951 25ml
EUR 425

Magnetic Beads for DNA Purification
M1502-5 5 ml
EUR 332.4

Magnetic Beads DNA Extraction Kit (Food)
MF004 each
EUR 3

Magnetic Beads DNA Extraction Kit (Food)
MF048 each
EUR 55

Magnetic Beads DNA Extraction Kit (Food)
MF096 each
EUR 99

Magnetic Beads DNA Extraction Kit (Blood)
MB004 each
EUR 3

Magnetic Beads DNA Extraction Kit (Blood)
MB048 each
EUR 40

Magnetic Beads DNA Extraction Kit (Blood)
MB096 each
EUR 75

Magnetic Beads DNA Extraction Kit (Plant)
MP004 each
EUR 3

Magnetic Beads DNA Extraction Kit (Plant)
MP048 each
EUR 55

Magnetic Beads DNA Extraction Kit (Plant)
MP096 each
EUR 99

Magnetic Beads DNA Extraction Kit (Bacteria)
ME004 each
EUR 3

Magnetic Beads DNA Extraction Kit (Bacteria)
ME048 each
EUR 60

Magnetic Beads DNA Extraction Kit (Bacteria)
ME096 each
EUR 110

Magnetic Beads for DNA size selection
AG0103 5 ml, 60 ml Ask for price
Description: The Magnetic Beads are ideal for DNA purification, concentration and size selection, along with next-generation sequencing library preparation kits.

Magnetic Beads
TRI-C86M05L 1000mL
EUR 8001

Magnetic Beads
TRI-C86M05M 200mL
EUR 1688.4

Magnetic Beads
TRI-C86M05S 100mL
EUR 844.2

Magnetic Beads-Based Plant Genomic DNA Kit
abx460019-1096tests 10 × 96 tests Ask for price

Magnetic Beads-Based Plant Genomic DNA Kit
abx460019-596tests 5 × 96 tests Ask for price

Magnetic Beads-Based Plant Genomic DNA Kit
abx460019-96tests 96 tests
EUR 437.5

Magnetic Beads-Based Blood Genomic DNA Kit
abx460020-1096tests 10 × 96 tests Ask for price

Magnetic Beads-Based Blood Genomic DNA Kit
abx460020-596tests 5 × 96 tests Ask for price

Magnetic Beads-Based Blood Genomic DNA Kit
abx460020-96tests 96 tests
EUR 437.5

FFPE Tissue DNA Extraction Kit - Magnetic Beads
K5011450 1 kit
EUR 261

Magnetic Beads-Based Tissue Genomic DNA Kit
abx460016-1096tests 10 × 96 tests Ask for price

Magnetic Beads-Based Tissue Genomic DNA Kit
abx460016-596tests 5 × 96 tests Ask for price

Magnetic Beads-Based Tissue Genomic DNA Kit
abx460016-96tests 96 tests
EUR 437.5

Magnetic Beads (RNA)
AG0104 5 ml, 60 ml Ask for price
Description: The Magnetic Beads (RNA)</strong> are automated for highly efficient RNA purification by specific adsorption.

Magnetic Beads Soil Genomic DNA Extraction Kit
MS004 each
EUR 3.5

Magnetic Beads Soil Genomic DNA Extraction Kit
MS048 each
EUR 65

Magnetic Beads Soil Genomic DNA Extraction Kit
MS096 each
EUR 120

Magnetic Beads-Based Bacteria Genomic DNA Kit
abx460017-1096tests 10 × 96 tests Ask for price

Magnetic Beads-Based Bacteria Genomic DNA Kit
abx460017-596tests 5 × 96 tests Ask for price

Magnetic Beads-Based Bacteria Genomic DNA Kit
abx460017-96tests 96 tests
EUR 437.5

Magnetic Beads Viral DNA/RNA Extraction Kit II
MV004 each
EUR 3

Magnetic Beads Viral DNA/RNA Extraction Kit II
MV048 each
EUR 72

Magnetic Beads Viral DNA/RNA Extraction Kit II
MV096 each
EUR 128

Magnetic Beads Viral DNA/RNA Extraction Kit II
MV480 each
EUR 590

Magnetic Beads-Based Buffy Coat Genomic DNA Kit
abx460015-1096tests 10 × 96 tests Ask for price

Magnetic Beads-Based Buffy Coat Genomic DNA Kit
abx460015-596tests 5 × 96 tests Ask for price

Magnetic Beads-Based Buffy Coat Genomic DNA Kit
abx460015-96tests 96 tests
EUR 437.5

Streptavidin Magnetic Beads
HY-K0208 5 mL
EUR 645.6

Streptavidin Magnetic beads
EA-IP-011M 1mL
EUR 241
Description: Primary Antibodies

Anti-HA magnetic beads
B26201 1 mL
EUR 579.6
Description: Anti-HA magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with high quality mouse IgG2b monoclonal antibody, used for co-immunoprecipitation and protein purification.

Anti-HA magnetic beads
B26202 5 mL
EUR 1742.4
Description: Anti-HA magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with high quality mouse IgG2b monoclonal antibody, used for co-immunoprecipitation and protein purification.

Anti-HA Magnetic Beads
HY-K0201 1 mL
EUR 334.8

SILICA MAGNETIC BEADS 1L
L5011001 1 liter
EUR 7260

Protein A Magnetic Beads
6507-1 each
EUR 314.4

Protein G Magnetic Beads
6517-1 each
EUR 314.4

Protein L Magnetic Beads
6537-1 each
EUR 352.8

Anti-Myc magnetic beads
B26301 1 mL
EUR 579.6
Description: Anti-Myc magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody.it is recommended to use for co-immunoprecipitation and protein purification.

Anti-Myc magnetic beads
B26302 5 mL
EUR 1742.4
Description: Anti-Myc magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody.it is recommended to use for co-immunoprecipitation and protein purification.

Protein A Magnetic Beads
HY-K0203 1 mL
EUR 148.8

Protein G Magnetic Beads
HY-K0204 5 mL
EUR 445.2

Protein A Magnetic beads
EA-IP-015M 1mL
EUR 105
Description: Primary Antibodies

Protein G Magnetic beads
EA-IP-016M 1mL
EUR 105
Description: Primary Antibodies

Protein L Magnetic beads
EA-IP-017M 1mL
EUR 105
Description: Primary Antibodies

Anti-Flag magnetic beads
B26101 1 mL
EUR 579.6
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.

Anti-Flag magnetic beads
B26102 5 mL
EUR 1742.4
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.

Anti-Flag Magnetic Beads
HY-K0207 1 mL
EUR 570

SILICA MAGNETIC BEADS 10ML
L5011010 10 ml
EUR 73

BlackPearl® (Magnetic Beads)
20161006-1 - Ask for price

BlackPearl® (Magnetic Beads)
20161006-2 - Ask for price

BlackPearl® (Magnetic Beads)
20161006-3 - Ask for price

Concanavalin A Magnetic Beads
K1308-1 1ml
EUR 44.8
Description: Protein & Immunology|Protein Purification and isolation

Concanavalin A Magnetic Beads
K1308-5 5x1ml
EUR 196.8
Description: Protein & Immunology|Protein Purification and isolation

Magnetic Beads™ Streptavidin
SMB-B01 5mg
EUR 149.8
Description: The Streptavidin-Magnetic Beads are 2.8 µm superparamagnetic particles covalently coupled to a highly pure form of streptavidin (SA). The beads can be used to capture the biotinylated proteins or other molecules, because Streptavidin (SA) has an extraordinarily high affinity for biotin with a dissociation constant (Kd) on the order of 10−14 mol/L, the Biotinylated molecules can bind to the SA irreversibly.Streptavidin is a tetrameric protein purified from the bacterium Streptomyces avidin, and exhibits high binding affinity for biotin. Able to bind one molecule of biotin with each subunit. Streptavidin (PI=6.0-7.5) has lower level of non-specific binding to various biological components at physiological pH than avidin (PI=7.4), resulting from its isoelectric point (PI).The Streptavidin-Magnetic Beads is easy to capture the biotinylated proteins or other molecules in Chemiluminescence procedures, and the bounded protein have no activity lost, this ready to use products could greatly save your protein coupling time and hassle, and help us get the best performance and highly reproducible results.

Concanavalin A Magnetic beads
EA-IP-014M 1mL
EUR 159
Description: Primary Antibodies

IP/CoIP Kit (Magnetic Beads)
EA-IP-K007M 50T
EUR 700
Description: Antibody Application Reagents

Protein A/G Magnetic Beads
6527-1 each
EUR 352.8

Protein A/G Magnetic Beads
HY-K0202 1 mL
EUR 157.2

Protein A/G Magnetic Beads
EA-IP-007M 1mL
EUR 80
Description: Primary Antibodies

Anti-c-Myc Magnetic Beads
HY-K0206 5 mL
EUR 1368

Anti-tGFP magnetic beads, 1ml
TA150039 1 ml Ask for price

Anti-tGFP magnetic beads, 5ml
TA150040 5 ml Ask for price

9E10, Anti-Myc Magnetic beads
TA150044 1 ml Ask for price

9E10, Anti-Myc Magnetic beads
TA150045 5 ml Ask for price

Magnetic Beads PCR Cleanup Kit
MC004 each
EUR 3

Magnetic Beads PCR Cleanup Kit
MC048 each
EUR 25

Magnetic Beads PCR Cleanup Kit
MC096 each
EUR 45

Anti-HA (Nanobody) Magnetic Beads
AE109 500μL
EUR 403

Anti-GFP (Nanobody) Magnetic Beads
AE079 500μL
EUR 312

Anti-Myc (Nanobody) Magnetic Beads
AE107 1000μL
EUR 213.2

Human FAP-coupled Magnetic Beads
MBS-K077 10mg
EUR 882.9
Description: The biotinylated FAP protein was conjugated to streptavidin magnetic beads. This pre-coupled magnetic bead product can capture the anti-FAP antibody from various assay systems. The beads are in uniform size, narrow size distribution with large surface area and unique surface coating, which can help you get the best performance and highly reproducible results. This FAP coupled magnetic beads will bring great convenience with minimum non-specific binding and developed protocols. This ready-to-use product could greatly save your time and hassle.

Anti-GFP (Nanobody) Magnetic Beads
MBS9143967-INQUIRE INQUIRE Ask for price

Human CD19-coupled Magnetic Beads
MBS-K005-10mg 10mg
EUR 4392.7
Description: Human CD19 protein is expressed from human 293 cells (HEK293). It contains AA Pro 20 - Lys 291(Accession # P15391-1).

Human CD19-coupled Magnetic Beads
MBS-K005-2mg 2mg
EUR 1427.9
Description: Human CD19 protein is expressed from human 293 cells (HEK293). It contains AA Pro 20 - Lys 291(Accession # P15391-1).

Human CD33-coupled Magnetic Beads
MBC-K008 2mg
EUR 2707.1
Description: Human CD33 protein is expressed from human 293 cells (HEK293). It contains AA Asp 18 - His 259(Accession # P20138-1(R69G)).

Human CD38-coupled Magnetic Beads
MBC-K010 2mg
EUR 2707.1
Description: Human CD38 protein is expressed from human 293 cells (HEK293). It contains AA Val 43 - Ile 300(Accession # P28907-1).

Human EGFR-coupled Magnetic Beads
MBE-K012 2mg
EUR 2707.1
Description: Human EGFR protein is expressed from human 293 cells (HEK293). It contains AA Leu 25 - Ser 645(Accession # P00533-1).

Human PSMA-coupled Magnetic Beads
MBP-K007 2mg
EUR 3349.1
Description: Human PSMA protein is expressed from human 293 cells (HEK293). It contains AA Lys 44 - Ala 750(Accession # Q04609-1).

Human ROR1-coupled Magnetic Beads
MBR-K009 2mg
EUR 2707.1
Description: Human ROR1 protein is expressed from human 293 cells (HEK293). It contains AA Gln 30 - Glu 403(Accession # Q01973-1).

Human BCMA-coupled Magnetic Beads
MBS-K004 2mg
EUR 2707.1
Description: Human BCMA protein is expressed from human 293 cells (HEK293). It contains AA Met 1 - Ala 54(Accession # Q02223-1).

Human CD19-coupled Magnetic Beads
MBS-K005 2mg
EUR 4312.1
Description: Human CD19 protein is expressed from human 293 cells (HEK293). It contains AA Pro 20 - Lys 291(Accession # P15391-1).

Human HER2-coupled Magnetic Beads
MBS-K006 500ug
EUR 2835.5
Description: Human HER2 protein is expressed from human 293 cells (HEK293). It contains AA Thr 23 - Thr 652(Accession # P04626-1).

Human ACE2-coupled Magnetic Beads
MBS-K013 2mg
EUR 2707.1
Description: Human ACE2 protein is expressed from human 293 cells (HEK293). It contains AA Gln 18 - Ser 740(Accession # Q9BYF1-1).

Human CD73-coupled Magnetic Beads
MBS-K022 2mg
EUR 3349.1
Description: Human CD73 Protein is expressed from human 293 cells (HEK293). It contains AA Trp 27 - Ser 549(Accession # P21589-1).

Human CD47-coupled Magnetic Beads
MBS-K023 2mg
EUR 2707.1
Description: Human CD47 Protein is expressed from human 293 cells (HEK293). It contains AA Gln 19 - Pro 139(Accession # Q08722).

Human CD3E-coupled Magnetic Beads
MBS-K026 2mg
EUR 2707.1
Description: Human CD3E Protein is expressed from human 293 cells (HEK293). It contains AA Asp 23 - Asp 126(Accession # P07766-1).

Human CD22-coupled Magnetic Beads
MBS-K052 2mg
EUR 4312.1
Description: Human CD22 Protein is expressed from human 293 cells (HEK293). It contains AA Asp 20 - Arg 687(Accession # P20273-1).

Human DLL3-coupled Magnetic Beads
MBS-K053 2mg
EUR 2707.1
Description: Delta-like protein 3 (DLL3) is a transmembrane protein that belongs to the Delta/Serrate/Lag-2 (DSL) family of Notch ligands.May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm. DLL3 protein is expressed on the surface of tumor cells but not in normal adult tissues.

Human uPAR-coupled Magnetic Beads
MBS-K076 2mg
EUR 2707.1
Description: Tumors are the result of uncontrolled proliferation of cells in different organs. Tumor development is a multistage process, that includes the generation of primary tumors, separation of tumors from primary sites, degradation of extracellular matrix (ECM), and distant metastasis of tumors. A variety of genes play important roles in the development of tumors, including the cell surface receptor urokinase-type plasminogen activator receptor (uPAR). uPAR is highly expressed in a variety of tumor cells, and a variety of signals regulated by uPAR play significant roles in tumor cell proliferation and metastasis, tumor-related glycolysis, the tumor microenvironment and angiogenesis. Studies have found that some specific drugs and antibodies have unique inhibitory effects on uPAR.

DDDDK-Tag Antibody (Magnetic Beads)
abx005594-100l 100 µl
EUR 250

Protein A/G/L Magnetic Beads
6547-1 each
EUR 405.6

Amylose BlackPearl® (Magnetic Beads)
20161009-1 - Ask for price

Amylose BlackPearl® (Magnetic Beads)
20161009-2 - Ask for price

Human PCSK9-coupled Magnetic Beads
MBS-K054 2mg
EUR 2707.1
Description: Proprotein convertase subtilisin/kexin type 9 (PCSK9) is also known as NARC1 (neural apoptosis regulated convertase), is a newly identified subtilase belonging to the peptidase S8 subfamily. Mouse PCSK9 is synthesized as a soluble zymogen, and undergoes autocatalytic intramolecular processing in the endoplasmic reticulum, resulting in the cleavage of its propeptide that remains associated with the secreted active enzyme with a broad alkaline pH optimum. This protein plays a major regulatory role in cholesterol homeostasis. PCSK9 binds to the epidermal growth factor-like repeat A (EGF-A) domain of the low-density lipoprotein receptor (LDLR), inducing LDLR degradation. PCSK9 may also have a role in the differentiation of cortical neurons. Mutations in this gene have been associated with a rare form of autosomal dominant familial hypercholesterolemia (HCHOLA3).

Human ASGR1-coupled Magnetic Beads
MBS-K055 2mg
EUR 2707.1
Description: ASGPR, a transmembrane C-type lectin, recognizes a wide variety of ligands that contain either terminal galactose (Gal) or N-acetylgalactosamine (GalNAc) residues and has been identified as a highly selective receptor on hepatocytes. The ASGR is composed of both a major (ASGR1) and minor subunit (ASGR2). ASGR1 has been shown to be efficiently targeted to the plasma membrane and to undergo constitutive endocytosis and recycling and found mainly expressed in the human liver.

Human ANGPT2-coupled Magnetic Beads
MBS-K035 2mg
EUR 2707.1
Description: Human ANGPT2 Protein is expressed from human 293 cells (HEK293). It contains AA Lys 275 - Phe 496(Accession # O15123-1).