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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