DBA Oligo, Inc. According to Soft-Go, independent reviewers, Oligo exceeds quality standards. Oligo 7 New Features.
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Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis.
The positions refer to the base numbers on the plus strand of your template i. Partial ranges are allowed. For example, if you want the PCR product to be located between position and position on the template, you can set forward primer "From" to and reverse primer "To" to but leave the forward primer "To" and reverse primer "From" empty.
Note that the position range of forward primer may not overlap with that of reverse primer. Optionally enter your pre-designed forward primer.
Primer Design with Oligo Primer Analysis Software v. 7
Always use the actual primer sequence i. Please enter the primer sequence only No any other characters are allowed. Optionally enter your pre-designed reverse primer. The Tm calculation is controlled by Table of thermodynamic parameters and Salt correction formula under advanced parameters. The default Table of thermodynamic parameters is "SantaLucia " and the default Salt correction formula is "SantaLucia " as recommended by primer3 program. This controls whether the primer should span an exon junction on your mRNA template.
The option "Primer must span an exon-exon junction" will direct the program to return at least one primer within a given primer pair that spans an exon-exon junction. This is useful for limiting the amplification only to mRNA. Minimal number of bases that must anneal to exons at the 5' or 3' side of the 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. This makes it easy to distinguish between amplification from mRNA and genomic DNA as the product from the latter is longer due to presence of an intron. This specifies the range of total intron length on the corresponding genomic DNA that would separate the forward and revervse primers. With this option on, the program will search the primers against the selected database and determine whether a primer pair can generate a PCR product on any targets in the database based on their matches to the targets and their orientations.
The program will return, if possible, only primer pairs that do not generate a valid PCR product on unintended sequences and are therefore specific to the intended template. Note that the specificity is checked not only for the forward-reverse primer pair, but also for forward-forward as well as reverse-reverse primer pairs. Primer-blast tries to find target-specific primers by placing candidate primers on unique template regions that are not similar to other targets.
However, in some cases, primer-blast cannot determine if a database sequence is an intended target or not, thus the user guidance might be helpful For example, when your template is a polymorphic form or a partial region of an entry in the search database, or when the database such as the nr contains redundant entries of your template. The "Automatic" option will ask for user guidance only when the program does not find sufficient unique template regions while the "User guided" option will always ask for user guidance if your template shows high similarity to any other database sequences.
Refseq mRNA: These genomes are among the best quality genomes available at NCBI. This database contains minimum redundancy in genome representation.
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For the eukaryotes, only one genome is included per species However, alternate loci of eukaryotic genomes are included where applicable. For other species, genomes from diverse isolates of the same species may be included. Mitochondrion genomes are included where applicable. Refseq RNA: Although sequences in this database are completely covered by the Refseq representative genomes database, it does not contain the alternate loci and therefore has even less redundancy than the Refseq representative genomes database. This database is recommended if you are not concerned about missing alternate loci or mitochondrion sequences.
You can choose to exclude sequences in the selected database from specificity checking if you are not concerned about these. Enter an organism name or organism group name such as enterobacteriaceae, rodents , taxonomy id or select from the suggestion list as you type. This will limit the primer specificity checking to the specified organism. It is strongly recommended that you always specify the organism if you are amplifying DNA from a specific organism because searching all organisms will be much slower and off-target priming from other organisms is irrelevant.
Click on "Add more organisms" label if you want to restrict to multiple organisms enter only one organism in each input box.
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You can use a regular entrez query to limit the database search for primer specificity. For example, enter a GenBank accession number to limit search to that particular sequence only Caution: Primer specificity stringency Primer must have at least 1 2 3 4 5 6 total mismatches to unintended targets, including at least 1 2 3 4 5 6 mismatches within the last 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 bps at the 3' end. The larger the mismatches especially those toward 3' end are between primers and the unintended targets, the more specific the primer pair is to your template i.
However, specifying a larger mismatch value may make it more difficult to find such specific primers. Try to lower the mismatch value in such case. This is another parameter that can be used to adjust primer specificity stringecy. If the total number of mismatches between target and at least one primer for a given primer pair is equal to or more than the specified number regardless of the mismatch locations , then any such targets will be ignored for primer specificity check.
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