Genetic Code

In the News..

15-11-2006

CLC bio New Hardware Accelerator

CLCbio have created the ‘CUBE’. A hardware unit which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer.

Using the Cube instead of BLAST, improves the quality of the data you're working with! read more..
The Tommi Melon

Primer Premier Features

New in Primer Premier

  • Cross species primers: Designs primers for amplifying sequences from multiple species.
  • 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.

Restriction Enzyme Analysis

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

Motif Analysis

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

Primer Design

  • 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 Database

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

Printing Features

  • 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.

Other Features

  • 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.