![]() actgcgccgTTGTAAAATGTATTATtAATtAGTTG), and primer dimer will include this additional sequence in its final dimer calculations. If fusion primers are added, they will be shownn in lower case letters in the final primer output (e.g. O Fusion Sequence (optional): the user may choose to add fusion sequences to the 5' end of the forward and/or reverse primer. O Report best primers only (optional): if this is selected, PrimerSuite will only report the primer pair which best fits all the parameters specified. Primers that are shown to contain "repeat regions" will be flagged in the result spreadsheet with "Repeat region found" in the relavent column. O RepBase Check (optional): checks the first 15 bases from the 3' end of each primer against an internal library of repetative sequences derived from Repbase. NOTE: In the current version, Primer Suite cannot design degenerate primers and if the progam detects any non-standard bases, the input sequence(s) will be rejected.īy default, Primer Suite has the bisulfite primer design function selected on start up.įor bisulfite primer design, it is recommended that users adjust the following parameters for optimal results, else the default values may be used (optimal conditions confirmed in the wet lab to produce quality primers). For this program, the DNA/RNA sequence(s) of interest can either be entered into the textarea in a FASTA format, uploaded as a fasta file (accepts *.fa, *.fsa, *.fasta). Primer Suite can design primers for both native or bisulfite-treated DNA. PrimerROC: accurate condition-independent dimer prediction using ROC analysis. PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR. We request that the use of any primers generated through PrimerSuite be cited as following: O PrimerPlex: Primer pooling module for arranging primers into different pools for multiplex PCR. ![]() O PrimerROC: ROC analysis for Primer Dimer formation. O PrimerDimer: Primer dimer detecting module. O FragCalc: calculates the ratio of fragements within a sample. O PrimerNucleosome: reports the nucleosome peaks related to input regions of interest. O PrimerSuite: Primer generating module for both genomic and bisulfite converted DNA. ![]()
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