ApE- A plasmid editor

Wayne Davis wdavis at biology.utah.edu
Mon Nov 22 12:17:44 EST 2004


Announcing the first public beta release (1.01) of new software for 
plasmid construction and visualization- ApE (a plasmid editor).
Features :
Runs in Windows, OS X-10.3, and Linux/Unix
Highlights restriction sites in the editing window
Higlights 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
Higlights 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 
indicated
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 annotaion 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 
efficiently
  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


downloads area available at:
http://www.biology.utah.edu/jorgensen/wayned/ape/

-- 
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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