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A plasmid Editor ApE is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly.
In addition, ApE provides a platform for creating visually appealing linear and circular plasmid maps. DNA visualization software must 1 annotate features and depict DNA features graphically, 2 simulate molecular cloning techniques and 3 generate visually appealing output for figures. Fundamentally this requires flexible annotation—applying names to a region, and visualization of functional regions—applying pictures to show the spatial relationships between sequence regions.
Every piece of the DNA should be annotated with its biologically relevant attributes. In addition, a biologist must be able to identify subsequences such as restriction enzyme recognition sequences, recombinase recognition sequences, and overlapping end sequences that are useful for particular recombinant techniques.
Good DNA software also provides powerful in silico simulation of common DNA manipulations, such as restriction digests or Gibson cloning. By manipulating DNA in silico , a biologist can ensure that recombinant constructs include functionally complete pieces that have the DNA in order and in frame. In other words, good software allows a researcher to synthesize a working plan.
This might be working backwards in silico from a desired product to determine the needed inputs. Conversely, it allows a researcher to start with a given set of available plasmids and work in the virtual laboratory to generate possible products.
Finally, visualization software can be invaluable for determining whether an analytic result—a DNA sequence, a diagnostic PCR or restriction digest—has generated the expected product. The scientist can use the software to align sequences or simulate gels of each step to confirm their work. Finally, good DNA software can generate visually pleasing output with a flexible level of detail. This representation should be easily exported in an open and widely used text or graphic format.
For example, text output can be used generate class reports, student theses, or manuscripts for publication. Similarly, graphical output can be used to generate meeting posters or slides for class reports or conference presentations.
Because of this critical need for visualization software, many DNA visualization programs have been written. Many of these are written by researchers themselves to solve their own needs in the lab. Often these are very powerful at solving a specific task, but can be lacking in broad application. Similarly, they are often dependent on a single operating system, and can sometimes have limited visual appeal in the graphic outputs. On the other hand, they are usually freely available, and so are very accessible to small groups and teaching labs.
At the other extreme, commercial ventures have written very powerful and flexible sequence visualization packages. Popular packages include Benchling. In order to have a wide customer base, they endeavor to have a complete set of analysis procedures and in silico reaction simulations. Because the visual output is usually a major factor in the product literature, the software has been carefully designed to generate visually appealing output.
All of this engineering takes programmer and designer time; as such, these packages are often cost prohibitive for individual laboratories, and almost always are out of range of a teaching laboratory.
A summary of some of the features in ApE and a selected set of other visualization programs is provided in Table 1. We have taken the long view to solving this problem. ApE is a freely available program written over the last 17 years by a molecular biologist for molecular biologists. Thus, it leverages the insider knowledge of what makes a successful DNA editing program.
Further, the long-timeframe approach has allowed the program to become both highly versatile and streamlined—ApE now rivals the commercially available packages in both its diversity of features and its visual outputs.
Importantly, unlike commercial packages, its free availability makes it well-suited for use in small labs or teaching labs. For Windows, the program is packaged into a self-contained tclkit Wippler, using the Starkit Developer eXtension sdx Thoyts, The Tclkit is a compiled binary generated by Ashok P.
The exe file was edited using Resource hacker Johnson, to contain a custom icon set and relevant version and copyright information. Bundled in the virtual filesystem of the exe file are copies of the ApE accessory files see below. The exe is compiled as an xbit application, and should run on versions of Windows between 98 and Windows The executable files in the bundle were generated from Tcl and Tk source Walzer, The current release is targeted to x86 architectures with OS versions The executable application bundle includes embedded Tcl and Tk frameworks, the Tcl script, copies of the ApE accessory files, a custom application icon and a MacOS property list file.
The wish binary is available by apt or apt-get on Debian systems. The usefulness of a program can be judged on three factors: flexibility of input, flexibility of data processing, and flexibility of output. To make ApE widely usable, we have endeavored to write procedures to read as many DNA sequence file types as possible.
ApE can also read Sanger sequencing chromatogram files in either the proprietary abi or open scf format. Sanger data is displayed as a scrollable and scalable graphic window, which can be used for aligning to a reference sequence.
This format is open and human-readable text, so saved data is not confined to a proprietary, binary format. In addition, many other programs and open-source libraries such as BioPerl or BioPython can read this format easily. Future editions of the program could allow viewing and editing these header lines.
Users can store base64 encoded versions of abi files as Genbank comment fields within an ApE file. Abi files linked in this way can be extracted and viewed with the standard abi viewer. The main sequence editing window of ApE. A The top section of the window shows basic properties of the sequence and selected region.
B The top section also shows the translation of the selected region. C The next pane shows a table of sequence features. Clicking on the arrowhead expands the description of the feature. D The next pane shows a list of all features under the mouse pointer here, hovering over F.
E The central region of the window contains the text of the sequence, with features highlighted in color. To the right is a vertical representation of these features in the currently displayed region and the scrollbar. On the far right is a representation of all of the features in the sequence. F When activated, the X-ray window shows a floating window containing a graphical representation of the line of text under the mouse pointer.
G The bottom of the window shows an editable sequence comment. To make ApE as flexible as possible for processing and visualizing user data, ApE stores several data files as human-readable text files. This allows users to store multiple versions of the files for different purposes, or trade useful variants with others. ApE uses this modular framework for the restriction enzyme set, the feature library, gel ladders, graphical arrowheads and user preferences.
Included with the distribution is a basic default set of enzymes, as well as several other enzyme database files, such as a set of all commercially available enzymes. DNA ladders for use in virtual agarose gels are stored in a file that can be edited using a ladder editor dialog within ApE. Arrowheads files are available to the user to customize the graphic map window. Finally, ApE includes a folder of feature definition library files. Feature definitions are designed to provide a rich and flexible matching paradigm.
Definitions include all of the characters of the IUPAC degenerate nucleotide code, with all sequence bases required to be within the degenerate set at each position for a match to be noted.
Finally, the definitions can contain either uppercase or lowercase characters. Once a match has been found, uppercase characters are noted as part of the feature, while lowercase characters are gaps in the feature. This allows for feature gaps such as introns, as well as searches for specific bases within a given context, for example common or important SNPs.
If a definition has only lowercase characters, all of the characters are included in the feature. Currently, ApE ships with default feature libraries for C.
Many of the procedures within ApE could be used as stand-alone, command-line functions or incorporated into other DNA analysis projects. ApE has several basic analysis functions such as reverse complement, complement, translate, reverse-translate, search with IUPAC degeneracy codes, search for amino acid sequences in a translated DNA sequence, and melting temperature calculation.
ApE also implements the DNA Strider algorithm for fast hexamer searching for restriction enzyme patterns Douglas, , which is faster at finding restriction enzyme sites than a regular expression search. Finally, ApE includes a procedure to search for PCR primer binding sites using a modification of the Strider hexamer lookahead algorithm. Because this algorithm is processor intensive, the alignment algorithm first uses a simple heuristic algorithm for doing a first-pass, block-based search for locally identical sequence matches, which are then used as boundaries for aligning non-identical blocks by the NW algorithm.
If the sequences have no major matching regions, the user can further specify a maximum value for mismatched regions to be aligned by the NW alignment algorithm. If a region between matching blocks has a product of lengths of each mismatched sequence region, the region is not aligned, and will be highlighted in black text in the resulting display. Once a pairwise alignment is made between the reference and each comparison sequence, the alignments are combined into a single alignment by adding gaps to each sequence; no attempt is made at multiple sequence alignment.
ApE has many ways to output and share data. For text-based visualizations or analysis windows, ApE can save an output file as plain text, or as formatted rich text format RTF files, which preserves color background highlighting and other text formatting.
For graphic visualizations of data, for example, graphic maps or virtual agarose gels, ApE can save the data in four formats: encapsulated postscript eps , scalable vector graphics svg , OpenXML-based Power Point pptx and portable document format pdf. An additional format, Windows Metafile wmf , is available on Windows systems.
All of these formats retain the information in vector format, so that they can be edited when opened in a vector editing program, such as Inkscape or Adobe Illustrator. Finally, on Mac and Windows, ApE is able to directly output windows to an attached printer with formatting preserved. For DNA Sanger sequencing files, the data are scaled to fit within the printed page, with a user-specified number of lines per page.
This wide variety of output formats and modalities should make ApE useful for saving an analysis in a laboratory notebook, for presenting the analysis on slides, for archiving the analysis in a database, or sharing the analysis on the internet. ApE has many functions for working with DNA. First, sequences can be annotated, applying names to regions of a sequence.
Features can be visualized in four ways: as text in a table at the top of a sequence, as a text appearing when pointing to a sequence, as a graphical representation when pointing to a sequence line, or as a small graphical summary at the right side of the sequence window.
In the main sequence window, features are indicated as highlighted text Figure 1E. In addition to the highlighted text, a tabular view of the features within a sequence is displayed Figure 1C.