Oligonucleotide design made simple. OligoFaktory Standalone Edition is a free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more Discover OligoFaktory Standalone Edition Design .
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- 10 links: Free Mac Software for Molecular Biologists
- 10 links: Free Mac Software for Molecular Biologists - Bitesize Bio
According to Soft-Go, independent reviewers, Oligo exceeds quality standards. Oligo 7 New Features. 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.
For each primer or primer pair, Oligo's various analysis windows show a multitude of useful data, such as DNA and RNA secondary structure, dimer formation, false priming and homology, internal stability, composition and physical properties. 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.
10 links: Free Mac Software for Molecular Biologists
Click on "Add more organisms" label if you want to restrict to multiple organisms enter only one organism in each input box. 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.
10 links: Free Mac Software for Molecular Biologists - Bitesize Bio
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. For examaple, if you are only interested in targets that perfectly match the primers, you can set the value to 1.
You can also lower the E value see advanced parameters in such case to speed up the search as the high default E value is not necessary for detecting targets with few mismatches to primers. Additionally this program has limit detecting targets that are too different from the primers You may need to choose more sensitive blast parameters under advance parameters if you want to detect targets with a higher number of mismatches than default. This specifies the max amplicon size for a PCR target to be detected.
If enabled, this program will NOT exclude the primer pairs that can amplify one or more mRNA splice variants from the same gene as your PCR template, thus making primers gene-specific rather than transcript-specific Note that it is NOT intended to generate primers that will amplify all variants. It only means that the primers may amplify one or more other slice variants, in addition to the one you have specified. Enabling this option will make it much easier to find gene-specific primers since there is no need to distinguish between splice variants. This option requires you to enter a refseq mRNA accession or gi or fasta sequence as PCR template input because other type of input may not allow the program to properly interpret the result.
This enables our new graphic display that offers enhanced overview for your template and primers. Maximum number of target sequences with unique sequence identifier blast will generate for primer-blast to screen for primer pair specificities. Note that the actual number of similarity regions or number of hits may be much larger than this for example, there may be a large number of hits on a single target sequence such as a chromosome.
Choose a higher value if you need to perform more stringent search. Expected number of chance matches in a random model. A higher E value should be used if you want more stringent specificity checking i. On the other hand, a lower E value is recommended if you are only interested in perfect or nearly perfect matches as this will significatly shorten the search time.
The minimal number of contiguous nucleotide base matches between the query sequence and the target sequence that is needed for BLAST to detect the targets. Set a lower value if you need to find target sequences with more mismatches to your primers.
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However this will increase the search time. The maximum number of candidate primer pairs to screen in order to find specific primer pairs The candidate primers are generated by primer3 program. Increasing this number can increase the chance of finding a specific primer pair but the process will take longer. The maximum number of PCR targets amplicons to be shown when designing new primers.
The maximum number of PCR targets amplicons to be shown when checking specificity for pre-designed primers. The maximum number of PCR targets amplicons to be found on any single sequence in the search database. The number of consecutive Gs and Cs at the 3' end of both the left and right primer.
The maximum stability for the last five 3' bases of a left or right primer. Bigger numbers mean more stable 3' ends. The maximum number of Gs or Cs allowed in the last five 3' bases of a left or right primer. The option "Use Thermodynamic Oligo Alignment" instructs Primer3 to use thermodynamic alignment models instead of old traditional secondary structure alignment for calculating the propensity of oligos to form hairpins and dimers while the option "Use Thermodynamic Template Alignment" instructs Primer3 to use thermodynamic alignment models instead of old traditional secondary structure alignment for calculating the propensity of oligos to anneal to undesired sites in the template sequence.
Or mark the source sequence with: Overlap junctions [? This requires that the left or the right primers to span a junction that is just 3' of any such positions. For example, entering "50 " would mean that the left or the right primers must span the junction between nucleotide position 50 and 51 or the junction between position and counting from 5' to 3'. You can also specify in the fields below the minimal number of nucleotides that the left or the right primer must have on either side of the junctions.
This option is useful if you want a primer to a span specific junction on the template. Epigenomics, 5 1 , Ulloa, P. Growth response and expression of muscle growth-related candidate genes in adult zebrafish fed plant and fishmeal protein-based diets. Zebrafish, 10 1 , pp. Ploenes, T. Agaras, B. Specific enumeration and analysis of the community structure of culturable pseudomonads in agricultural soils under no-till management in Argentina. Applied Soil Ecology, 61 null , pp. Auguste, A. Loss of R-spondin1 and Foxl2 amplifies female-to-male sex reversal in XX mice.
Sexual development: Avolio, M. Gidekel, M. Novel genes and uses thereof, expression profile of colon, gastric and pancreatic cancer. Bahamondes, V.
Arthritis and rheumatism, 63 10 , pp. Balic, I. Molecular and physiological study of postharvest rachis browning of table grape cv Red Globe. Postharvest Biology and Technology, 72 null , pp. Journal of autoimmunity, 39 , pp.
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Begley, J. Assessment and monitoring tools for aerobic bioremediation of vinyl chloride in groundwater. Remediation Journal, 20 1 , pp. Bravo, N. Castro, I. Rheumatology Oxford, England , 51 3 , pp. Effect of emamectin benzoate on transcriptional expression of cytochromes P and the multidrug transporters Pgp and MRP1 in rainbow trout Oncorhynchus mykiss and the sea lice Caligus rogercresseyi. Lipopolysaccharide signaling in the carotid chemoreceptor pathway of rats with sepsis syndrome.
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Seebacher, ed. PloS one, 7 9 , p. Gautam, P. Proteomic and transcriptomic analysis of Aspergillus fumigatus on exposure to amphotericin B. Antimicrobial agents and chemotherapy, 52 12 , pp.