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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. The table is sortable by feature name, direction, GenBank feature type and location. If a feature has GenBank qualifiers, those qualifiers are displayed within the table under drop-down rows that can be opened or closed.
The table context menus allow the editing of many aspects of feature display, such as the name, highlight color, and display priority a. A similar context menu is available in the other columns of the table to quickly edit the other properties of each feature.
For example, the location of the feature, that is, the range of bases included in the feature, as represented by numbers, can be edited. To edit a feature more extensively, a user can double-click any table row or alternatively right click the sequence text directly.
An important aspect of ApE is that features can be added to a file by using a predefined or user-defined feature library to scan the entire sequence. Feature libraries consist of lines of text referred to here as feature definitions. Each feature definition in the library is compared against the entire sequence, one by one, and if a match is found, the feature name and formatting defined in the library are applied to that part of the sequence.
Thus, raw sequences can be rapidly converted to a table of feature names and base ranges. This modular approach benefits both the data sharing as well as the data preservation roles of ApE. Feature libraries can be exchanged between lab members or between lab groups. For example, collections of PCR primers can be stored as feature libraries and used to annotate any number of sequence files. Because feature visualization is so important, ApE provides three ways to see what features are assigned to a piece of text.
First, placing the mouse pointer over any character displays the feature names of all features assigned to that character Figure 1D. Second, an X-ray window mode shows a semi-transparent overlay of the features and highlighted restriction recognition sites Figure 1F. This window follows the mouse and updates with scrolling the text. Third, there is a small graphical map of features along the right edge of the sequence Figure 1E.
Finally, features can be hidden from the current display without deleting the feature from the feature table. This modular approach allows the user to visualize features in many different contexts. ApE is a sequence editor, and contains powerful general and DNA specific text editing tools, including basic text input, sequence search, ORF search, specialized copy and paste functions, and brief instantaneous analysis of selected text.
The sequence can be linear or circular, as specified with a button at the top of the window Figure 1A. Sequence-related metadata or user notes or comments can be entered into a text box at the bottom of each sequence window Figure 1G.
ApE has a search function specialized for the needs of molecular biologists. However, the search can be specified to find DNA sequences using the search input as degenerate bases, single letter amino acid codes, or literal bases. Further, the search can be specified to match just the top DNA strand, or can search for the match in both strands, and can match the characters in a case-sensitive or case-insensitive search.
In addition to a text-matching search function, ApE has an open-reading-frame-based search function. This search can find the next or previous open reading frame relative to the current insertion cursor. A user can filter ORFs requiring a minimum length, requiring starting with a methionine or the next codon after the next stop, and requiring the ORF to be on either the top or bottom DNA strand.
This can be used to make a complete record of the sequence in a lab notebook, an email, or a laboratory database, for example. These clipboard files can be re-imported and will open as a new sequence window.
These features are displayed in the top area of the window as the text selection is changed. At times, the user may need other ways of visualizing aspects of a sequence that go beyond the basic feature highlighting in the sequence window.
Data tracks include restriction enzyme recognition sequences, position index, translation, bottom strand sequence, and feature regions. The user can then copy or save the window as a plain-text or rich-text RTF representation for archiving, sharing, or presenting the sequence. The translation can be formatted as single or three-letter codes, with optional spacing, line numbering and corresponding DNA sequence.
The analysis includes the number of translated amino acids and the predicted molecular weight of the protein. In order to aid in visualizing the most potentially relevant open reading frames, the user is given the option of specifying a minimum cutoff for highlighting regions between stop and start or between adjacent stop codons.
The user can then click on any highlighted region to select the corresponding region of the parent sequence. This function converts all of the sequence features and selected enzyme cut sites into a vector map Figure 2.
The map can be either circular Figures 2A,B or linear Figures 2C,D , depending on the nature of the sequence region depicted. Feature and enzyme elements are linked to their parent sequence regions, so that mouse clicks on a graphical element cause the corresponding region to be selected in the parent. Graphical maps of a sequence. A A circular map of pUC19, with colored features and restriction enzyme sites. B A different circular map of the same sequence file showing a variety of user-configurable display properties.
C A linear map of a region of the same pUC19 file. D Another linear map of the same region, showing a variety of user-configurable display properties. Each graphic window can be saved into four vector-based file formats: encapsulated postscript eps , scalable vector graphics svg , XML-based Power Point pptx , and portable document format pdf.
By exporting into four different popular vector-graphic formats, ApE visualizations can be imported into many other programs that can represent vector graphics. For example, sequence maps can be read into Inkscape, Adobe Illustrator, OpenOffice Draw, or LibreOffice Draw for writing papers or lab reports, or posted directly to a website as svg for sharing on the web.
ApE has several tools, described in later sections, that use restriction enzyme sites as input. First, we describe how restriction enzyme sites are selected. The central switchboard for restriction site recognition in ApE is the enzyme selector dialog.
The selection dialog presents a central window with a list of enzyme names Figure 3A. Enzymes can be selected by clicking on each name, while shift-clicking will select the individual site uniquely. Enzyme comments are displayed as the pointer hovers over the list. At the top of the dialog is a window selection area, where the user can select any of the currently open sequence windows, and can elect to analyze either the entire sequence or just the currently selected region.
ApE determines the number of recognition sites within the selection, which is displayed next to the enzyme name. Some restriction enzymes do not cut sites that overlap with E. ApE maintains a database of overlapping configurations that are not cut. Thus, the user can choose to calculate the number of enzyme sites as though the DNA is or is not from a methylated source.
The enzyme selector dialog and virtual agarose gels. A The enzyme selector dialog. The bands from each lane are shown in a table. C The same gel window, but showing detailed information for a single ApaLI band highlighted by hovering the mouse over the band. The calculator works by setting a desired number of sites in the current window, as well as membership in an enzyme group. The enzymes that meet both the number and group membership filters are previewed as underlined in the selection list.
Because the enzyme selector serves as a central place to select enzymes that are used in other tools, the dialog supplies a shortcut to several of these tools as a convenience. These appear at the bottom of the enzyme selection dialog. In the X-ray window, these highlighted enzyme sequences show not only the recognition site, but also the cut sites, as a small tick mark upwards at the position of the top strand cut, and downwards for the bottom strand cut.
Placing the pointer over a gel band brings forward a table in the analysis window and a miniature map of the features and digestion sites in the parental sequence. The table shows each band as the cut site location, band size and approximate mass percent of the total digest that the band represents, and the map highlights the sequence of the band.
Clicking on a band will select the region of the sequence represented by the band. Gel bands can be used as inputs in the Gibson reaction dialog by drag-and-drop into the dialog, and can be used as inputs into the ligation dialog by simply clicking a band when the dialog is opened. In this dialog, each gel lane is represented by a row. Each row is either a DNA or ladder.
Each DNA row can then be digested with single or multiple enzymes by activating a checkbox representing the specific enzyme column in the row. For some applications it can be useful to identify sequences that can be mutated to generate a new restriction enzyme recognition site.
ApE has two functions that do this kind of analysis. Instead, it allows the user to specify a maximum number of base changes allowed for the generation of the site.
In both analysis results, the sequence is live-linked to the parent sequence, so that clicking on any base representing a base in the sequence selects that base in the parent window. The tool dialog initially prompts the user for a DNA sequence window or gel band. The information for that DNA populates the dialog with a picture of the overhanging end sequences, and a mini-map of the sequences in the fragment. If the fragments have compatible ends, the user can choose to complete the reaction, which will generate the product of the ligation as a new sequence window.
The new sequence will have a comment section that lists all of the input plasmids and digestions used to generate the product. If the ends are not compatible, the dialog will not allow the reaction to be completed. The user can choose to reverse any of the fragments or modify the ends of the fragment with several common modification reactions. The restriction-ligation assembler tool. A Graphic maps of the input sequence files for the planned reaction left and the product right.
The two fragments are then dragged into the Restriction-Ligation Assembler tool dialog. The tool then generates the product shown in A. The Golden Gate reaction is similar to a basic restriction-ligation reaction; however, the use of type IIS restriction enzymes adds distinct requirements and thus ApE has distinct tools for dealing with this type of reaction.
Unlike traditional ligation reactions, Golden Gate reactions can join as many fragments as unique overhanging sequences can be designed.
In fact, successful fragment reactions have been demonstrated with empirically validated orthogonal overhangs Pryor et al. ApE has distinct workflows for designing Golden Gate reactions to create a defined construct and assembling a Golden Gate reaction using existing constructs.
The dialog gives the user a choice of available type IIS enzymes, and then the option of selecting DNA fragments to be ligated. The algorithm then uses a random walk to search for a set of the most orthogonal overhangs, and presents a set of PCR primers to generate them. Because the algorithm can get caught in local minima, the user is given the option to restart the search with a new random seed if a non-optimal solution was found.
A new sequence window is created containing the desired reaction product, including new features containing the primer sequences. These primer sequences are also added to the file comment, both as a list of PCR reactions including primer pairs and templates, as well as a list of primers in a format compatible with online oligonucleotide ordering systems. The Golden Gate Designer tool. A Graphic maps of the input sequences left and output sequence right.
The user chooses one to three type IIS restriction enzymes. Once an enzyme has been selected, the assembler searches open sequences for any fragments that are flanked by oppositely oriented sites and for compatible overhang sequences.
The assembler then gives the user a drop-down list of all possible fragments that are in a closed circular assembly. If multiple fragments are possible at a given position, a new dropdown menu is presented to the user. The process is repeated until the circle is closed. The user can choose to generate the conceptual product in a new sequence window.
The new window will contain a sequence comment listing all of the plasmid sequence files used in the Golden Gate reaction that generated that sequence. The Golden Gate Assembler tool. A A graphic map of two SapI restriction fragments as designed in Figure 5 to be used in a Golden Gate reaction left , and the product of the reaction right. A third, very flexible and effective, DNA assembly method is based on long homologous end hybridization.
This class of methods includes Gibson assembly Gibson et al. Gel bands are automatically set to be non-PCR fragments. Once all of the fragments are selected, the user is prompted to review and modify the homologous overlap at each fragment junction. Each junction is displayed at the top of the review window, showing the new forward and reverse primers, and the template sequences. The user can choose to incorporate new, non-templated bases into the gap between the fragments.
The Gibson Designer tool. A Graphic maps of the two input sequences left and the output sequence right. The tool then steps through both Gibson junctions, allowing fine-grained design of each. Finally, the tool generates the sequence shown on the right in A.
A modular assembly method is recombinase-mediated assembly. The most popular of these methods is the Gateway cloning system from Invitrogen a brand of ThermoFisher. Once a prototype is chosen, the algorithm searches all open windows to find fragments that contain the correct sites in the correct orientation to be a substrate for the chosen reaction.
If multiple compatible sequences are found for a fragment, the user can choose between the options via the drop-down menu. Once all required sequences are found and selected, the simulated reaction generates a product plasmid. As for other reaction simulators, a list of the input sequences and the reaction performed is added to the sequence comment box of the product. Gateway reaction. A Graphic map of the input sequences for a Gateway BP reaction left and the product of the recombination right.
The tool then generates the product sequence, represented by the map in A. Although most users only perform the basic Gateway reactions as described in the product literature, the Gateway recombination reaction is very flexible and has been adapted to specific use cases. Similarly, pWormgatePro allows users to build a similar hairpin construct for C. ApE allows users to design new reaction prototypes to accomplish any DNA recombination reaction in silico.
Amplification by PCR is the most critical method in molecular biology laboratories. A major role of the tool is to use a primer database to search a template sequence for primer binding sites. The database can be loaded from a text file formatted as an ApE feature library file. Sequences in the system clipboard can be formatted as simple DNA sequences or as tab delimited name-sequence pairs, each on a new line. PCR Reaction tool. A graphic map of this product is shown in A.
By default, the tool then shows a list of primers that match at a single site within the template. Primers in the list can then be selected or deselected by the user. Selected primers are shown in their approximate location and direction on a mini-map diagram in the center of the window. Can accommodate four peoples 2 double beds. Situated in full town center close to restaurants, Each piece is handmade and unique, and cannot be exactly replicated.
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Adobe Creative Suite CS is a discontinued software suite of graphic design , video editing , and web development applications developed by Adobe Systems. On May 6, , Adobe announced that CS6 would be the last version of the Creative Suite,    and that future versions of their creative software would only be available via their Adobe Creative Cloud subscription model.
Adobe also announced that it would continue to support CS6 and would provide bug fixes and security updates through the next major upgrades of both Mac and Windows operating systems as of The following table shows the different details of the core applications in the various Adobe Creative Suite editions.
Each edition may come with all these apps included or only a subset. Adobe Stock launched in Adobe sold Creative Suite applications in several different combinations called “editions”, these included:. Adobe Prelude and Adobe Encore are not released as standalone products. Adobe Encore is available as part of Adobe Premiere Pro. In March , it was reported that Adobe would no longer sell boxed copies of the Creative Suite software, instead offering digital downloads and monthly subscriptions.
Creative Suite helped InDesign become the dominant publishing software, replacing QuarkXPress , because customers who purchased the suite for Photoshop and Illustrator received InDesign at no additional cost. Adobe shut down the “activation” servers for CS2 in December , making it impossible for licensed users to reinstall the software if needed. In response to complaints, Adobe then made available for download a version of CS2 that did not require online activation, and published a serial number to activate it offline.
Adobe Creative Suite Production Studio previously Adobe Video Collection was a suite of programs for acquiring, editing, and distributing digital video and audio that was released during the same timeframe as Adobe Creative Suite 2.
The suite was available in standard and premium editions. Macromedia Studio was a suite of programs designed for web content creation designed and distributed by Macromedia. After Adobe ‘s acquisition of Macromedia, Macromedia Studio 8 was replaced, modified, and integrated into two editions of the Adobe Creative Suite family of software from version 2. Some Macromedia applications were absorbed into existing Adobe products, e.
FreeHand has been replaced with Adobe Illustrator. Director and ColdFusion are not part of Adobe Creative Suite and will only be available as standalone products. The final version of Macromedia Studio released include:. Adobe Creative Suite 3 CS3 was announced on March 27, ; it introduced universal binaries for all major programs for the Apple Macintosh ,  as well as including all of the core applications from Macromedia Studio and Production Studio.
Some Creative Suite programs also began using the Presto layout engine used in the Opera web browser. Adobe began selling CS3 applications in six different combinations called “editions. The latest released CS3 version was version 3.
CS3 included several programs, including Dreamweaver , Flash Professional , and Fireworks that were developed by Macromedia , a former rival acquired by Adobe in Adobe dropped the following programs that were previously included in CS2 from the CS3 software bundles: . Adobe had announced that it would continue to develop Audition as a standalone product, while GoLive had been discontinued. Adobe GoLive 9 was released as a standalone product on June 10, Adobe Audition 3 was announced as a standalone product on September 6, Adobe had discontinued ImageReady and had replaced it with Fireworks, with some of ImageReady’s features integrated into Photoshop.
Audition became part of the Creative Suite again in CS5. Adobe CS4 was also developed to perform better under bit and multi-core processors.
Two programs were dropped from the CS4 line-up: Adobe Ultra , a vector keying application which utilizes image analysis technology to produce high quality chroma key effects in less than ideal lighting environments and provides keying of a subject into a virtual 3D environment through virtual set technology, and Adobe Stock Photos. Below is a matrix of the applications that were bundled in each of the software suites for CS Following the release of CS5 in April , Adobe changed its release strategy to an every other year release of major number installments.
The update helped developers optimize websites for a variety of tablets, smart phones, and other devices. At the same time, Adobe announced a subscription-based pay service as an alternative to full purchase. Not all products were upgraded to CS5. Below is a matrix of the applications that were bundled in each of the software suites for CS5. On May 5, , during the opening keynote of its Adobe MAX conference, Adobe announced that it was retiring the “Creative Suite” branding in favor of “Creative Cloud”, and making all future feature updates to its software now appended with “CC” instead of “CS”, e.
Photoshop CC available via the Creative Cloud subscription service rather than through the purchasing of perpetual licenses. Customers must pay a subscription fee and if they stop paying, they will lose access to the proprietary file formats ,   which are not backward-compatible with the Creative Suite   Adobe admitted that this is a valid concern .
Individual subscribers must have an Internet connection  to download the software and to use the 2 GB of provided storage space or the additionally purchased 20 GB  , and must validate the license monthly. Adobe’s decision to make the subscription service the only sales route for its creative software was met with strong criticism   see Creative Cloud controversy.
In addition to many of the products formerly part of the Creative Suite one product, Fireworks, was announced as having reached the end of its development cycle ,  Creative Cloud also offers subscription-exclusive products such as Adobe Muse  and the Adobe Edge family,  Web-based file and website hosting, Typekit fonts, and access to the Behance social media platform.
New versions with major feature updates have been released regularly, with a refresh of the file formats occurring in October Adobe also announced that it would continue to offer bug fixes for the CS6 products so that they will continue to run on the next versions of Microsoft Windows and Apple OS X.
From Wikipedia, the free encyclopedia. Discontinued software suite. Main article: Adobe Creative Cloud. Archived from the original on Retrieved Ars Technica. Digital Photography Review. As of January 9, Creative Suite is no longer available for purchase. Retrieved March 13, Archived from the original on May 9, Archived from the original on April 1, Adobe Systems. Archived from the original on 23 March Retrieved 10 January Adobe Creative Suite 2. Archived from the original on January 8, Archived from the original on January 10, Mobile Magazine.
Archived from the original PDF on Opera Software ASA. Archived from the original on March 23, Archived from the original PDF on October 30, Archived PDF from the original on May 14, Beta news. Photoshop CS4. Archived from the original on February 18, PC World. John Nack on Adobe. Conversations Web log. Investor relations.
Labs download. The next Web. Life Hacker. Creative Bloq. Mac life. Tech crunch. Adobe Creative Suite and Creative Cloud. Adobe Inc. Category Commons. Hidden categories: Articles with short description Short description is different from Wikidata. Namespaces Article Talk. Views Read Edit View history. Help Learn to edit Community portal Recent changes Upload file. Download as PDF Printable version. Wikimedia Commons. September 29, ; 18 years ago Microsoft Windows , OS X.
IA limited , PowerPC limited , x Adobe Creative Cloud. Digital media creation and editing. Replaced by Creative Cloud desktop app.