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- In_silico_PCR abstract "In silico PCR refers to computational tools used to calculate theoretical polymerase chain reaction (PCR) results using a given set of primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome.These tools are used to optimize the design of primers for target DNA or cDNA sequences. Primer optimization has two goals: efficiency and selectivity. Efficiency involves taking into account such factors as GC-content, efficiency of binding, complementarity, secondary structure, and annealing and melting point (Tm). Primer selectivity requires that the primer pairs not fortuitously bind to random sites other than the target of interest, nor should the primer pairs bind to conserved regions of a gene family. If the selectivity is poor, a set of primers will amplify multiple products besides the target of interest.The design of appropriate short or long primer pairs is only one goal of PCR product prediction. Other information provided by in silico PCR tools may include determining primer location, orientation, length of each amplicon, simulation of electrophoretic mobility, identification of open reading frames, and links to other web resources.Many software packages are available offering differing balances of feature set, ease of use, efficiency, and cost. Possibly the most widely used would be e-PCR, freely accessible from the National Center for Biotechnology Information (NCBI) website. On the other hand, FastPCR, a commercial application, allows simultaneous testing of a single primer or a set of primers designed for multiplex target sequences. It performs a fast, gapless alignment to test the complementarity of the primers to the target sequences. Probable PCR products can be found for linear and circular templates using standard or inverse PCR as well as for multiplex PCR. VPCR runs a dynamic simulation of multiplex PCR, allowing for an estimate of quantitative competition effects between multiple amplicons in one reaction.A primer may bind to many predicted sequences, but only sequences with no or few mismatches (1 or 2, depending on location and nucleotide) at the 3' end of the primer can be used for polymerase extension. The last 10-12 bases at the 3' end of a primer are sensitive to initiation of polymerase extension and general primer stability on the template binding site. The effect of a single mismatch at these last 10 bases at the 3' end of the primer depends on its position and local structure, reducing the primer binding, selectivity, and PCR efficiency.".
- In_silico_PCR thumbnail In_silico_PCR_example_result_(jPCR_result).png?width=300.
- In_silico_PCR wikiPageExternalLink insilico.ehu.es.
- In_silico_PCR wikiPageExternalLink tools.
- In_silico_PCR wikiPageExternalLink webpcr.appspot.com.
- In_silico_PCR wikiPageExternalLink csPCR.
- In_silico_PCR wikiPageExternalLink e-pcr.
- In_silico_PCR wikiPageID "34964561".
- In_silico_PCR wikiPageLength "7371".
- In_silico_PCR wikiPageOutDegree "21".
- In_silico_PCR wikiPageRevisionID "702276595".
- In_silico_PCR wikiPageWikiLink Amplicon.
- In_silico_PCR wikiPageWikiLink Category:Bioinformatics.
- In_silico_PCR wikiPageWikiLink Category:Nucleic_acids.
- In_silico_PCR wikiPageWikiLink Complementary_DNA.
- In_silico_PCR wikiPageWikiLink DNA.
- In_silico_PCR wikiPageWikiLink Electrophoresis.
- In_silico_PCR wikiPageWikiLink FastPCR.
- In_silico_PCR wikiPageWikiLink Genome.
- In_silico_PCR wikiPageWikiLink Hybridization_probe.
- In_silico_PCR wikiPageWikiLink Inverse_polymerase_chain_reaction.
- In_silico_PCR wikiPageWikiLink Multiplex_polymerase_chain_reaction.
- In_silico_PCR wikiPageWikiLink National_Center_for_Biotechnology_Information.
- In_silico_PCR wikiPageWikiLink Nucleic_acid_secondary_structure.
- In_silico_PCR wikiPageWikiLink Nucleic_acid_thermodynamics.
- In_silico_PCR wikiPageWikiLink Open_reading_frame.
- In_silico_PCR wikiPageWikiLink Polymerase_chain_reaction.
- In_silico_PCR wikiPageWikiLink Polymerase_chain_reaction_optimization.
- In_silico_PCR wikiPageWikiLink Primer_(molecular_biology).
- In_silico_PCR wikiPageWikiLink Transcriptome.
- In_silico_PCR wikiPageWikiLink File:In_silico_PCR_example_result_(jPCR_result).png.
- In_silico_PCR wikiPageWikiLinkText "''in silico'' PCR".
- In_silico_PCR wikiPageWikiLinkText "Electronic PCR".
- In_silico_PCR wikiPageWikiLinkText "In silico PCR".
- In_silico_PCR wikiPageUsesTemplate Template:Reflist.
- In_silico_PCR subject Category:Bioinformatics.
- In_silico_PCR subject Category:Nucleic_acids.
- In_silico_PCR type Biomolecule.
- In_silico_PCR type Biomolecule.
- In_silico_PCR type Biostatistic.
- In_silico_PCR type Polymer.
- In_silico_PCR comment "In silico PCR refers to computational tools used to calculate theoretical polymerase chain reaction (PCR) results using a given set of primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome.These tools are used to optimize the design of primers for target DNA or cDNA sequences. Primer optimization has two goals: efficiency and selectivity.".
- In_silico_PCR label "In silico PCR".
- In_silico_PCR sameAs Q4112082.
- In_silico_PCR sameAs PCR_in_silico.
- In_silico_PCR sameAs m.0j43plj.
- In_silico_PCR sameAs Виртуальная_ПЦР.
- In_silico_PCR sameAs Q4112082.
- In_silico_PCR wasDerivedFrom In_silico_PCR?oldid=702276595.
- In_silico_PCR depiction In_silico_PCR_example_result_(jPCR_result).png.
- In_silico_PCR isPrimaryTopicOf In_silico_PCR.