![]() the oligo pair-annealing score." Not very helpful in my view. the secondary structure score and parameters pertaining to oligo-pairs such as e.g. Applied Biosystems Sequence Scanner Software v2.0 (Download). The algorithm considers both the parameters pertaining to single oligos, such as e.g. (Edit: From the help menu: "CLC Main Workbench employs a proprietary algorithm to rank primer and probe solutions. However, since you are quite free to set a multitude parameters, I guess that the hits are scored mainly based on fitting these as well as the alignment with the homolog sequences. I didn't really get any insight into the algorithm that CLC uses to determine primers in the manual. While checking the software options I saw that most people recommend Primer3 in this context. However, I didn't use it for TaqMan probes yet. Bioinformatics features in CLC Sequence Viewer Multiple alignment of DNA, RNA, and proteins Two proprietary algorithms ClustalW Muscle T. Phylogeny CLC Main Workbench allows for creation and visualization of phylogenetic trees and associated metadata. CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options. Assembly CLC Main Workbench allows you to import, view, edit, and analyze results from automated sequencing machines. It offers convienient options to design primers from alignments that are able to discriminate between rather homolog sequences. Sequence hits can easily be downloaded and analyzed further. Since I am used to do primer design in the CLC Main Workbench that would obviously be my first choice. The N-terminal sequences of the proteins were sequenced by using the Applied Biosystems Procise cLC sequencing system (model 492cLC Life Technologies. I want to design primers/probes for a TaqMan application.
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