Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor algorithm. Primers are screened for secondary structures,dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in a ranked order. Load the gene of interest from NCBI, select a search range, sit back and let Primer Premier pick the best possibleprimers for you.
Primer Premier 6.0 For Mac
Download: https://shoxet.com/2vKjI9
Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design.
With Primer Premier, you can load sequences from dbSNP and have the primers designed flanking the SNP selected. Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files. After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry.
Primer Premier is a comprehensive primer design application.PCR primer design- design primer pairs for PCR and multiplex experiments. Cross species- Amplify sequences from multiple species.Pathogenic detection- Locate oligos in highly conserved regions. Allele specific- Exclusively amplify a single member of a set of related sequences.Degenerate- Start with an amino acid sequence, reverse translate and design oligos in regions of low degeneracy automatically.Nested/multiplex- Checking homology among multiple candidate oligos. Restriction enzyme and motif analysis- Select from the database of over 800 enzymes and 200 common motifs. Clustal W alignments- Load the aligned sequences after performing ClustalW alignment using any resource, including EBI.Multiple sequence alignment- Use the popular Clustal W algorithm to align sequences from your desktop (available in Windows version only).Algorithm- Calculates Tm using Breslauer values. Long PCR- Handles sequences up to 50 KB.
Primer Premier is an application to design and analyze PCR primers. Primer Premier 's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order.
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.
Primer Premier software combines design of primers for various PCR applications under one common platform. The software supports design of degenerate primers on alignments for amplifying a related set of nucleotide sequences for detecting many common traits amongst organisms and to determine heredity.[1]
The software has a built-in nucleotide-protein and protein-nucleotide sequence translator which can be used for designing degenerate primers for codons that code for multiple amino acid sequences. It is also understood that the primers designed by Primer Premier are effective and confirm to the design guidelines laid for designing primers for housekeeping genes with a high G+C%.[3]
You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.
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