Features

Tagged Primer Design

Design Primers: Design thousands of primer pairs optimized for Gateway®, BD In-Fusion™, TOPO® and epitope systems or add functionally useful tags to design primers for any expression system.

Design Nested Primers: Design primers to successfully amplify ORFs with nested PCR. The outer primer is designed in the UTR in a region of no significant homology. The inner primer pair amplifies the PCR product generated by the outer primer pair.

Design Primers for Fusion Products: Designs primer for generating N and C terminal fusion products with functionally useful tags.

Lightning Speed: Processes three hundred 10kb sequences in approximately 2 minutes.

Maintain Reading Frame: Automatically maintain the reading frame of the ORF to be amplified when adding tags.

Avoid Termination Codon: Automatically checks for inframe termination codon.

High Throughput Primer Search

Algorithm: Calculates primer Tm using nearest neighbor thermodynamic algorithm.

Primer Rating: Uses statistical optimization techniques to output only the best rated primer pair.

Comprehensive Search Criteria: Primers are screened for their thermodynamic properties as well as secondary structures.

Uniform Conditions: Optimizes all primers in a single search run for uniform PCR cycling conditions.

Sequencing Primer Design

Design Primers: Sequencing primers are designed across amplicons with a user defined interval between forward primers. Reverse primers stagger on the opposing strands.

Design Primers for In vitro Expression Studies

Generate Precise Transcripts: Design primers to generate sense or antisense transcripts for in vitro expression studies.

Data and Database Management

Projects: Multiple projects can be created. Data of multiple experiments can be easily managed by creating separate project for each experiment.

Application Database: Maintains a local database for sequence information and search results.

Web Integration

Web Integration: Quickly retrieves batches of ORF sequences directly into the program from Entrez using accession numbers or GI numbers.

Input/Output

Input Formats: Supports sequences in GenBank, and FASTA formats. GenBank and FASTA formatted files can contain multiple sequences for batch loading.

View Output: Primer search results can be viewed and manipulated in any spreadsheet program like Microsoft Excel and Lotus123.

Load Output: Tab delimited format of the output file can be easily loaded into any database.