I may need to put ApE on the Apple store and start charging for it to get around this in the future.
The current Mac version has a bad bug on Mavericks. I've made a Mavericks-specific side branch that fixes the bug but doesn't run as well in non-Mavericks systems. Please chose the version for your OS. The two Mac versions should rejoin into a single version in the near future.
Runs in Windows (XP, Vista, 7 and 8) and Mac (OS X v10.5 and above)
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:
Alignments (including ABI sequences)
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
Click the icons at the top of the page for the latest version (version 2.0.x is out of alpha testing)
You can now export genomic regions from Wormbase directly: In the upper right drop-down menu button, select "Download Track Data". Click the "Configure..." button. Dump selected features using version 3 Across currently visible region. Check "Save to File". Check "Embed DNA sequence". UNCHECK "Include track configuration data". Click "Go". Open the resulting .gff file in the latest ApE.
Alternatively, you can export a genomic region (from the genome viewer) as a FASTA formatted file (using the menu on the upper left). You can add the feature tracks by downloading the GFF3 feature track files using the same menu. In ApE, open the FASTA file, then use the Features menu to open the GFF3 track info.
Another way to go is to take the gene model (from a gene page), paste it into an ApE window and then select all, make a new feature (Feature menu), and in the edit feature window that appears press the "upper case only" button.
If you think that ApE doesn't find all of the ClaI sites (or XbaI or BclI) that you KNOW are present in your sequence, turn off the Dam/Dcm methylation on your sequence and try again.
See here for more information.
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