Up to 40 custom oligonucleotide sequences can be specified.
Most display colors can be customized.
Options to include Type I and III enzymes, homing endonucleases and nicking enzymes.
Options to ignore individual types of methylation.
Many DNA sequences are pre-computed and selectable from the pull-down menus
on the front page.
Projects can be saved to a local file and uploaded later.
Stored projects can be deleted from our server.
Input:
New input file formats: GCG, DNAStar and EMBL.
Ambiguous nucleotides are allowed in the input sequence, up to 5 in any 20 nt window.
Option to process only a specified region of the input sequence.
Display:
All NEB isoschizomers are displayed on the maps. Previously only one
example was shown.
RE maps can be saved as high quality raster or vector images.
Option to list enzymes based on the number of sites produced. The list can be
ordered alphabetically or by cut frequency.
Option to list the sites of a given enzyme along with the flanking sequences.
Option to list all sites in the sequence.
Lists can be saved to a local text file.
On the lists the cut sites are indicated within the recognition sequences.
Basepair highlighting is selectable on the nucleotide level display.
Option to specify the exact zoom coordinates.
After zooming to a region the sequence of that region can displayed or
re-submitted as a separate project.
ORFs:
The genetic code of the submitted sequence is selectable.
Option to mark the sequence as a fragment. This causes partial ORFs to be
displayed even if their start/stop codon is missing.
ORFs can be edited, deleted or new ones defined.
Silent mutagenesis routine to introduce unique sites in a selected ORF
without altering the protein sequence. These sites can be introduced
into the sequence by a single mouse click.
Digests:
On the enzyme selection page, options added to list enzymes by their site
length and cut frequency.
"Pick all" option for each group on the enzyme selection page.
Option to select the enzymes used for the previous digest.
Option to list the selected enzymes and their sites along with the flanking
sequences.
New gels have been added and some parameters of the virtual gel are now
adjustable.
