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

SimVector 4 Features

Plan Cloning Experiments

  • Design Gateway Cloning Experiments: Using SimVector you can perform both the BP and the LR reactions that constitute Gateway® Cloning. The donor vector and the expression vector are required for the BP reaction and for generating an entry clone. An entry vector and a destination vector are required for the LR reaction and for generating an expression vector.
  • Design TA Cloning Vector: SimVector makes it easy to design TA cloning experiments. The TA cloning wizard accepts both commercial T-vectors or restriction designed T-vectors and combines them with the modified PCR product. You can then generate a highly accurate recombinant DNA plasmid map.
  • Perform Restriction Cloning: This cloning technique requires restriction enzymes to cut the vector molecule and the molecule to be cloned. SimVector performs restriction enzyme analysis and allows you to filter, annotate and map the restriction enzymes on the desired sequences.
  • Perform Restriction Enzyme Analysis: SimVector identifies restriction enzyme recognition sites in DNA sequences for restriction site mapping. A comprehensive database of over 1000 restriction enzymes is used for the restriction analysis. Two modes of enzyme filtering are provided to specify the parameters for restriction analysis. Enzyme filtering enables you to set the enzyme criteria to match your experimental requirements. For convenience, enzyme sets from more than 20 commercial providers are included.

Draw Catalog Quality Plasmid Maps

  • Draw Plasmid Maps: Draw publication quality plasmid maps with SimVector.
  • Multiple Cloning Site (MCS) Display: SimVector identifies the MCS's by interpreting GenBank header annotations when available, or you can specify them manually.
  • It even has the smarts to list only the enzymes that cut within the MCS and nowhere else. This special format we call the Bracket View.
  • Catalog Quality Vector Graphics: Generates plasmid map images in vector graphic format for Adobe Illustrator 10 and Microsoft PowerPoint 2002.
  • Export Web Ready Images: Exports high resolution plasmid map images in JPEG, PNG and TIF format for easy addition to web sites and exports images are ready to host pages.
  • Graphical Entrez Features: Transforms GenBank annotations to graphical features (linear and circular sequence map).
  • Create Vectors: Create a vector map without knowing its sequence

Customize Vector Maps

  • Easy Styling: Choose from hundreds of fonts, colors, styles and fill patterns for restriction enzymes and features with a click of a button.
  • Color Theme: Define your own custom color theme and apply it over and over again.
  • Marquee Select: Group select objects to quickly set styles for all.
  • Linear and Circular Views- Produces both circular and linear vector maps.
  • Zooming: Zoom in for detailed graphics or out for an overview.
  • Text: Add text to annotate the plasmid maps.

Printing

  • Print: Print the vector map, the sequence, the detailed analysis result, and the sequence notes added.

Sequence Analysis:

  • ORF Search: You can find ORFs in the chosen reading frames, identified with the selected start and stop codons, and compliant to the specified minimum length. With a click of a button, you can now ensure that the construct remains in-frame after cloning. The graphical ORF display is always ready for reference and further analysis.
  • Sequence Translation- Translate sequences for simulating expressed proteins and to check for possible reading frame errors.
  • Restriction Enzyme Analysis- You can perform restriction enzyme analysis on complete sequences as well as on fragments by specifying a range. The results of the restriction enzyme analysis are mapped on the circular or linear vectors, displaying the positions of restriction enzyme cleavage sites.
  • Restriction Site Mapping- Restriction site mapping is the first step in planning an experiment. SimVector offers complete control over all key parameters to perform the restriction enzyme analysis. Restriction site mapping is easy with SimVector. Just select the enzymes you would like use, analyze and let SimVector draw a high quality restriction site map. SimVector analyzes your maps for over a 1000 restriction enzymes and upto 24 commercially available restriction enzyme sets.
  • Restriction Enzyme Filtering- Select restriction enzymes by overhang, recognition site length, and other properties.
  • Custom Restriction Enzyme Set- Create your own enzyme set for repeated analysis.