Extensive Primer Design Support

Primer Premier is a comprehensive primer design tool for PCR, hybridization, cross species, sequencing and allele specific polymerase chain reaction.

Integrated Alignment

Primer Premier fully integrates multiple sequence alignment for consensus or species specific PCR primer design using the well proven, widely used ClustalW algorithm.

Degenerate and Multiplex Primer Design

With Primer Premier you can start with an amino acid sequence, reverse translate and design primers in regions of low degeneracy automatically. Primer Premier designs highly specific primers for multiplex experiments and analyzes them for homologies.

Sequence Analysis

Along with PCR primer design, use Primer Premier to analyze your templates using an extensive built-in database of common enzymes and motifs. You can even add, delete or edit enzyme and motif information to customize the program for your experiments.

Comprehensive Reports

View and print comprehensive reports on hairpin, dimer, false priming, optical activity and internal stability of your designed primers.

Versatile Primer Analysis

Primer Premier lets you analyze pre-designed and published primers. You can also design primers for site directed mutagenesis.

Features

• Cross species primers: Designs primers for amplifying sequences from multiple species.
  (For Real Time qPCR cross species primers, try AlleleID®)
  
• ClustalW multiple sequence alignment: Aligns multiple sequences using ClustalW 1.7 algorithm.
  
• Minority consensus: Generates consensus sequence using degenerate bases.
  
• Alignment editor: Manually insert/delete/move gaps in an alignment.
  
• File Format Support: Now supports various file formats like GenBank, NBRF/PIR, EMBL/SWISSPROT and FASTA.

Sequence Editor

• Long PCR: Handles sequences up to 50 KB.
  
• Alternate views: View sequence as sense, anti-sense, or double stranded.
  
• Importing sequences: Complimenting or reversing sequence while cut, copy, paste.
  
• Voice readback: Multimedia readback of sequences.
  
• Translations: Translate and reverse-translate between DNA and protein sequences, easy switching between the original and translated sequences.
  
• Edit codon table: Add new codon tables or choose from the universal or comprehensive set of mitochondria codon tables.
  
• Grouping: Displays bases in groups of 3 or 10.
  
• Finds occurrences of specified sequence.
  

• Enzyme filtering: Filter enzymes based on overhang sequence, recognition site length, or heat inactivation.
  
• Enzyme editing: Adds and edits custom enzymes.
  
  

• Motif analysis: Scan the sequence for nucleic acid motifs.
  
• Motif editing: Edits already existing motifs or adds new ones.
  
  

• PCR/ Hybridization/Sequencing primer search: Locates optimal primers for PCR, hybridization, or sequencing.
  
• Automatic search: automatic search automatically relaxes stringency to locate the best primers available on the sequence.
  
• Degenerate Primer Design: Reverse translate a protein sequence and design primers in regions of low degeneracy. Based on our research published in: Vinay Singh, Sita Naik, “A Program for Design of Degenerate Primers from a Protein Sequence”, Biotechniques, February 1998.
  
• Manual Search: Allows researcher to set specific primer properties and locates all primers with these properties.
  
• Secondary structures: Analyzes primers for hairpins, self-dimers, cross-dimers, and false priming sites.
  
• Multiplex/Nested primers: Check primer pools and preexisting primers for cross homologies.
  
• False priming: Check primers against a directory of sequences for false priming.
  
• Site directed mutagenesis: Easily incorporate enzyme sites and silent mutations.
  
• Analyze existing primers: Paste in any primer sequence for analysis, check for its binding sites on sequence.
  
• Primer rating: Ranks both individual primers and primer pairs based on priming efficiency.
  
• Comprehensive primer report: Prints comprehensive report for pairs and individual primers.
  
• Printing of all secondary structures: Print all secondary structures for a primer.
  
  

• Primer databases: Store multiple sets of primers with easy primer ordering.
  
• Order forms: Easily order primers using customizable order form.
  

• Comprehensive primer report: Prints comprehensive report for pairs and individual primers.
  
• Multiplex/nested primers: Prints searched and selected primers over the sequence symbolically and selected primers in tabular format along with their cross dimers.
  
• Printing of all secondary structures: Print all primer secondary structures.
  
  

• Hybridization time: Predict hybridization time of probes.
• Optical activity: Calculates optical activity of primer in nmol/A260 and g/A260.
  
• Molecular weight: Calculates primer molecular weight.
  
• Pasting oligonucleotides: Oligonucleotides can be pasted as is, reversed, complemented or reverse complemented.
  
• Primer Design tutorial