• 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