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

Xpression 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.