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new cross-platform plasmid editing software

new cross-platform plasmid editing software - Protocols and Methods Forum

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Old 11-22-2004, 03:11 AM
Wayne Davis
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Default new cross-platform plasmid editing software

I'm making available the first public beta release (current version
1.02) of new software I've written for plasmid construction and
visualization: ApE (A plasmid Editor).

This is a program similar in concept to programs like DNAStrider.
It is designed for making restriction maps (text-based and graphic,
linear and circular), virtual restriction digests, PCR primer finding,
DNA translation, silent site mutagenesis, and other frequent operations
useful to cloners, using a straightforward graphical user interface.
It can run in OS X (10.3 or higher), all Windows versions, and UNIX/Linux.
It is currently free, but if interest develops, I might put up a paypal
donation option for people who want to support my efforts.
I'd like to know if people find it useful, what bugs they find, and what
other features they'd like to see.

downloads are available at:
[Only registered users see links. ]

The ApE features most users have found the most useful have been (1)
almost all elements of analysis windows (translations, alignments,
graphic plasmid maps) are linked back to the original sequence by a
simple double-click; (2) user-defined feature libraries for automatic
annotation; and (3) a calculator-like restriction enzyme selector.

(1) Linking means that clicking on an EcoRI site on the graphic map
takes you directly to the EcoRI site in the sequence editing window.
Likewise, double clicking on a band in the virtual gel selects the DNA
representing that band in the editing window.
(2) User-defined feature libraries mean that users can tell the program
what relevant features look like using a simple interface and store
these definitions in simple files. One can then automatically annotate
any sequence by searching for these features in an editing window. This
means, for example, that by setting up a feature library that contains
all of your primer sequences, you can search and generate a graphic
display of all primer binding locations within a given sequence. You can
also show where features such as replication origins, selectable
markers, genes, promoters etc. are located in your clone. The features
are highlighted in color in the editing window and represented as arrows
on graphic maps.
(3) The calculator-like enzyme selector window simplifies many cloning
tasks. In the most basic mode, it allows the user to specify which
enzymes will be used in an analysis by simply clicking on the desired
enzyme names. However enzymes can be selected and de-selected based on
their sequence properties (blunt, 6-cutter, etc.) and their cut
frequency in a given sequence. In this way, simple questions like "which
enzymes in this MCS are not present in my gene", or "which enzymes can I
use to distinguish the desired construct from the parent vector, or the
reverse orientation" are answered easily. Further, the program can be
told whether the DNA is Dam/Dcm methylated (as is DNA extracted from
most E. coli strains) or not (as are PCR products) and adjusts the
restriction site analysis accordingly.

Other ApE Features :
Runs in Windows, OS X-10.3, and Linux/Unix
Highlights restriction sites in the editing window
Highlights text using pre-defined and custom feature libraries
Shows translation, Tm, %GC, ORF of selected DNA in real-time
Reads DNA Strider, Fasta, Genbank and EMBL files
Highlights and draws graphic maps using feature annotations from genbank
and embl files
Directly BLASTs selected sequence at NCBI or wormbase

Creates graphic restriction maps- linear or circular with features
Connects graphic and text features with double click
Saves graphics as encapsulated postscript,scalable vector graphics, or
windows metafiles
Copy graphics as metafiles (MS windows only)

Virtual restriction digest
Draws pre-defined and user-defined DNA ladders
Connects bands to text by double-click

Reads ABI sequencing trace files

Selects sites matching multiple criteria (union/intersection- cut
frequency, site type) in all open windows
Deals with Dam/Dcm methylation of DNA

Other Features:
Uses custom feature libraries, which allow:
quick annotation of sequence
quick searching and highlighting of all available primers that you (or
others) have that hybridize to a sequence
sequence to be annotated and visualized in multiple ways quickly and
graphic maps that show primer binding sites and all interesting
sequence features
Translates sequences with optional DNA alignment
Finds potential primers matching user criteria (length, Tm, %GC,
self/other complementarity)
Aligns two DNA sequences using Needleman-Wunsch
Finds translationally silent restriction sites
Draws graphic ORF maps

Wayne Davis

Department of Biology
University of Utah
257 South 1400 East
Salt Lake City, UT 84112-0840
(801) 585-3692

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