ApE 1.17

ApE is an easy to use plasmid analysis and editor software for your Mac.

Here are some key features of "ApE":

· Runs on Mac OS X (10.3, 10.4 and 10.5), Windows (tested on 98, XP, NT), and Linux/Unix
· Highlights restriction sites in the editing window
· Accurately reflects Dam/Dcm blocking of enzyme sites
· 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
· Saves files as DNA Strider-compatible or Genbank file format
· Highlights and draws graphic maps using feature annotations from genbank and embl files
· Directly BLASTs selected sequence at NCBI or wormbase
· Text map shows DNA sequence, translation, and features as text-based graphics
· Creates graphic restriction maps- linear or circular with features indicated
· Connects graphic and text features with hyperlink double click
· Saves graphics as encapsulated postscript or scalable vector graphics
· Copy and save graphics as Windows 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
· Sequences in ABI traces can be aligned directly to a reference sequence, with the alignment hyperlinked back to te trace.
· Selects sites matching multiple criteria (union/intersection- cut frequency, site type) in all open windows
· Selects sites that cut more often in one sequence than another (for snip-SNP detection or diagnostic digests)
· Has user defined enzyme grouping to distiguish eg. enzymes currently in stock.
· Allows users to define new enzymes by name and recognition site
· Imports DNA Strider format files (simple enzyme, site lists) available from REBASE
· Most analysis windows are hyperlinked to their corresponding sequences, including: Graphic Maps, Text maps, Virtual Digests, Alignments (including ABI sequences), Silent Sites, Translation, Primer Find
· Uses custom feature definition 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 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 (or any combination of sequence and ABI trace), with the alignment hyperlinked to the original sequence
· Finds translationally silent restriction sites
· Draws graphic ORF maps