MethSpec: a simple and efficient tool for evaluation of MSP primer specificity
MethSpec is a simple tool that carries out evaluation of MSP primer specificity based on primer pair's sequences and parameters such as: primer concentration, ion concentration and annealing temperature. There are two alternative strategies for evaluation of MSP primers specificity used by MethSpec. The first one assumes that last nine bases at 3' end are relevant for primer specificity (9-mer approach) while the other approach uses algorhythm proposed by Miura et al ( Miura et al., 2005).
The software determines SDSS (Specificity-Determining SubSequence) for forward and reverse primer and calculates stability of duplexes, expressed as dG value, that are formed with bisulfite modified methylated (target sequence), bisulfite modified unmethylated and appropriate native DNA sequence. The software carries out bisulfite modification of the input promoter sequence and localization of the primers inside it. By comparation of original input sequence and bisulfite modified one, MethSpec determines positions of modified cytosines inside primer's sequences. According to these positions program knows where mismatches are located. Alternatively, mismatch position can be specified by user. In this case position of modified cytosines should be marked with lowercase letter.
You are welcome to use our free for evaluation of MSP primer specificity. Just input the primer sequences and submit data.
MethSpec is free open source software (FOSS) released under BSD licence.
Standalone JAVA application with source code and documentation can be downloaded from here:
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