Primer Express Software Version 3.0 Download
Rosaura Woolf
Minimal and maximal number of bases that must anneal to exons at the 5' or 3' side of the junction Help This specifies the minimal number of bases that the primer must anneal to the template at 5' side (i.e., toward start of the primer) or 3' side (i.e., toward end of the primer) of the exon-exon junction. Annealing to both exons is necessary as this ensures annealing to the exon-exon junction region but not either exon alone. Note that this option is effective only if you select "Primer must span an exon-exon junction" for "Exon junction span" option.
Minimal number of nucleotides that the left or the right primer must have at the 5' or 3' side of the junctions Concentration of monovalent cations Help The millimolar concentration of salt (usually KCl) in the PCR. Primer3 uses this argument to calculate oligo melting temperatures.
The Primer Express Software v3.0 allows you to design your own primers and probes. Primer Express Software provides customized application-specific documents for absolute/relative quantitation and allelic discrimination, and also includes an improved workflow for allelic discrimination assay designs.
Primer3 was a complete re-implementationof an earlier program:Primer 0.5 (Steve Lincoln, Mark Daly, and EricS. Lander).Lincoln Stein championed the idea of making Primer3 a software component suitable for high-throughputprimer design.
Web interface bySteve Rozen
The express() function is required to create an Express application. This is a top-level function included in the Express module at the time you download Express into the root folder of your project by issuing this command:
The express() function has several methods, each of which offers developers several options to use within a given method. For instance, express.static(index). express is the function. static is the method. And (index) is the option unique to the static method. This line of code sends the client the index file within the root folder. The default item it sends is the index.html file.
Transfer rate is expressed in transfers per second instead of bits per second because the number of transfers includes the overhead bits, which do not provide additional throughput;[49] PCIe 1.x uses an 8b/10b encoding scheme, resulting in a 20% (= 2/10) overhead on the raw channel bandwidth.[50] So in the PCIe terminology, transfer rate refers to the encoded bit rate: 2.5 GT/s is 2.5 Gbps on the encoded serial link. This corresponds to 2.0 Gbps of pre-coded data or 250 MB/s, which is referred to as throughput in PCIe.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) represents a universally expressed reference gene that has many biological roles in addition to its function in glycolysis. A GAPDH assay has been developed for the accurate normalization of feline messenger RNA (mRNA) expression [10], and this assay was recently validated and compared to other potential feline mRNA reference gene assays [11]. Subsequently, the GAPDH assay was also applied as quality control to test for the integrity of the gDNA and the absence of PCR inhibitors [10, 12, 13]. One report suggested that a single copy of the GAPDH pseudogene is present in the feline genome and that the feline GAPDH assay can therefore be used to quantify cell number in feline samples [14]. However, no information on the exact position or the sequence of this GAPDH pseudogene was provided [14]. In contrast, a variable number of GAPDH pseudogenes has been reported for other organisms [15, 16].
An approach combining sequencing and bioinformatics was chosen to investigate the presence of potential GAPDH pseudogenes in the domestic cat genome. The potential target sequence of the GAPDH qPCR assay was amplified and cloned, and 15 clones were sequenced: 10 from cat B8 and 5 from cat 15. The sequencing of these 15 clones yielded 11 distinct sequences similar to that of the feline GAPDH mRNA (GenBank: NM_001009307). Eight different sequences were found within the target region of the primers and/or the hydrolysis probe of the GAPDH TaqMan assay (Figure 1). Overall, the sequence identity ranged from 82% (cat 15, clone 20: cat 15_20, Figure 1) to 96% (cat B8, clone 9: cat B8_9) in comparison to the reference sequence (GenBank: NM_001009307).
In this report, we describe the detection of several GAPDH-like sequences that are characteristic for processed GAPDH pseudogenes in the domestic cat genome. Based on the assumption that there is only one copy of the GAPDH pseudogene in the domestic cat genome [14], the GAPDH qPCR assay that was previously designed to amplify GAPDH mRNA/complementary DNA (cDNA) [10] was regularly used to determine the cell number of input gDNA. However, in our experience, the analysis of gDNA samples resulted in a lower amplification efficiency compared to cDNA (unpublished observations); we hypothesized that this might occur due to mismatches between the primers and/or hydrolysis probe and the gDNA sample. Thus, we performed a sequence analysis of the binding region of the primers and the hydrolysis probe of the GAPDH assay. The sequencing of 15 different clones comprising the GAPDH assay sequence revealed 11 different GAPDH-like sequences; however, none exhibited 100% similarity to the GAPDH mRNA sequence (GenBank: NM_001009307). It is possible that there are additional GAPDH pseudogenes present in the feline genome that were not detected in the present study because the sequencing was restricted to 15 clones. The use of an alternative sequencing technique (deep-sequencing rather than cloning followed by Sanger dideoxy sequencing) may provide a broader picture of the GAPDH-like sequences present in the cat genome. Furthermore, the primer binding sites chosen within the GAPDH sequence may have additionally restricted the number of recognized GAPDH pseudogenes. Thus, the number of GAPDH pseudogenes or GAPDH-like sequences in the feline genome may have been underestimated in our study. However, our sequencing results readily demonstrate that more than one feline GAPDH pseudogene is present in the genomic DNA of feline cells, and the GAPDH pseudogene sequences differed from the GAPDH mRNA sequence to some extent.
This primer provides an approachable introduction to OWL 2, including orientation for those coming from other disciplines, a running example showing how OWL 2 can be used to represent first simple information and then more complex information, how OWL 2 manages ontologies, and finally the distinctions between the various sublanguages of OWL 2.
The W3C OWL 2 Web Ontology Language (OWL) is a Semantic Web language designed to represent rich and complex knowledge about things, groups of things, and relations between things. OWL is a computational logic-based language such that knowledge expressed in OWL can be reasoned with by computer programs either to verify the consistency of that knowledge or to make implicit knowledge explicit.OWL documents, known as ontologies, can be published in the World Wide Web and may refer to or be referred from other OWL ontologies. OWL is part of the W3C's Semantic Web technology stack, which includes RDF [RDF Concepts] and SPARQL [SPARQL].
The key goal of the primer is to help develop insight into OWL, its strengths, and its weaknesses. The core of the primer is an introduction to most of the language features of OWL by way of a running example. Most of the examples in the primer are taken from a sample ontology (which is presented entirely in an appendix). This sample ontology is designed to touch the key language features of OWL in an understandable way and not, in itself, to be an example of a good ontology.
Frequently, the information that two individuals are interconnected by a certain property allows to draw further conclusions about the individuals themselves. In particular, one might infer class memberships. For instance, the statement that B is the wife of A obviously implies that B is a woman while A is a man. So in a way, the statement that two individuals are related via a certain property carries implicit additional information about these individuals. In our example, this additional information can be expressed via class memberships. OWL provides a way to state this correspondence:
Until now we focused on classes and properties that were merely used as building blocks for class expressions. In the following, we will see what other modeling capabilities with properties OWL 2 offers.
This would for example allow to deduce for arbitrary individuals A and B, where A is linked to B by the hasChild property, that B and A are also interlinked by the hasParent property. However, we do not need to explicitly assign a name to the inverse of a property if we just want to use it, say, inside a class expression. Instead of using the new hasParent property for the definition of the class Orphan, we can directly refer to it as the hasChild-inverse:
On the other hand, a property can also be asymmetric meaning that if it connects A with B it never connects B with A. Clearly (excluding paradoxical scenarios resulting from time travels), this is the case for the property hasChild and is expressed like this:
While the last example from the previous section implied the presence of an hasAncestor property whenever there is a chain of hasParent properties, we might want to be a bit more specific and define, say, a hasGrandparent property instead. Technically, this means that we want hasGrandparent to connect all individuals that are linked by a chain of exactly two hasParent properties. In contrast to the previous hasAncestor example, we do not want hasParent to be a special case of hasGrandparent nor do we want hasGrandparent to refer to great-grandparents etc. We can express that every such chain has to be spanned by a hasGrandparent property as follows:
In OWL 2 a collection of (data or object) properties can be assigned as a key to a class expression. This means that each named instance of the class expression is uniquely identified by the set of values which these properties attain in relation to the instance.
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