Ape a plasmid Editor a Tcl/Tk script written by M. Wayne Davis Copyright 2003-2004, all rights reserved All beta versions are not for re-distribution, and should be obtained directly from the author




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ApE

A plasmid Editor

a Tcl/Tk script written by M. Wayne Davis

Copyright © 2003-2004, all rights reserved

All beta versions are NOT for re-distribution, and should be obtained directly from the author.

All trademarks and registered trademarks are the property of their respective owners.



Table of Contents


Installation 4

Windows 98/ME/XP/2000 4

OS X 4

Linux 4


User Preferences Folders 4

DNA Windows 5

Menus 6

File 6


Edit 6

Enzymes 6

ORFs 7

Features 7



Tools 7

Windows 7

Help 7

Toolbar 8



ABI Window 9

Preferences Dialog 10

Preferences Dialog: General 10

Preferences Dialog: Color 10

Preferences Dialog: ABI 10

Preferences Dialog: Files 11

Preferences Dialog: Filetypes (Windows Only) 11

Find Sequence Dialog 11

Enzyme Selector Dialog 12

New Enzyme Dialog 14

Edit Enzyme Dialog 15

Image Output Options 16

Circular Graphic Map 16

Linear Graphic Map 17

Edit Ladders Dialog 19

List Enzymes Dialog 19

Silent Sites 20

Text Map Window 21

Translate Dialog 22

Translation Window 22

ORF Map Window 23

DNA Features 24

New Feature Window 24

List Features Window 24

Feature Display Properties Dialog 25

Edit Feature Library 25

Find Primer Dialog 26

Primer Window 26

Align Sequences Dialog 28

Sequence Alignment Window 28

BLAST Sequences Dialog 30

AA Info Window 30

Standard Genetic Code Window 31

Associated Files 32

ApE_Defaults 32

Default_Enzymes.txt 32

Default_Features.txt 32

DNA_ladders.txt 33

Icons and images (directory) 33

lib (directory- windows only) 34

Msgs (directory) 34

ApE in other languages 35

References 36

Copyright and Disclaimer 37

Copyrights of included technologies 37

Installation


ApE is currently distributed as a ZIP compressed file for Windows, OS X (10.3), and Linux. There are three different ZIP files: Windows, Linux and OS X. Select and download the appropriate version for your computer

Windows 98/ME/XP/2000


In windows, you can unzip the file and it will make a folder called ApE inside your “Program Files” folder.

There is a shortcut in the folder you can use to run the program. (If you move the folder somewhere besides “C:\Program Files”, you need to look in the "Properties" for the shortcut and change the directory from "C:\Program Files\Ape\" to where ever you moved the folder (It's in the shortcut twice, so change both instances). You can copy or move this shortcut to any location on your computer for quick access to ApE.

After you run the program you can go to the menu option "Edit/Preferences" to set up file extension associations, so that .str files, for example, can be opened by double-clicking. It is important that you make the file association using the mechanism inside ApE, as other file association mechanisms might not work.

To uninstall, just uncheck the file associations in preferences. The folder can then be thrown away. You may also throw away all user preferences folders (see below)


OS X


In OS X, the file can just be unzipped to an application file. You can drop this into your Applications folder and onto your Dock. You can make it the default application for opening files with .str, .dna, .seq extensions.

Linux


The file should be unzipped into a new directory. You will need to go to http://www.equi4.com/tclkit.html and download the appropriate Tclkit version for your Linux distribution. Tcl/Tk script AppMain.tcl can then be run using the command line “tclkit AppMain.tcl [dna_file]”.

User Preferences Folders


All versions of ApE after 1.08 store a user preference directory for each user that has ever run ApE. You can delete all of these directories if you uninstall ApE. In Windows 95/98 they are usually located in C:\WINDOWS\Profiles\[username]\Application Data, in Windows XP they are in C:\Documents and Settings\[username]\Application Data. On the Mac, they are in [user home]/Library/Preferences. In Linux the directories are in [user home]/.ApE/

All user preferences files should be cross-platform compatible. Default color schemes might look odd on a different platform. If this happens, go to Preferences/Colors and select default colors to correct the issue.



DNA Windows




Menus

File


New

Open

Duplicate

Close

Save

Save As

Exit

Edit


Undo

Cut/Copy/Paste

Cut/Copy/Paste rev-com

Preferences

Select All

Select From To

Jump to:

Find:

Find Again

Clear Find

->UPPERCASE

->lowercase

UPPER<->lower

Reverse Complement

Circular<->linear

Set Origin

Linearize at Insert Site

Enzymes


Enzyme Selector…

Selection Only

Graphic Map

Graphic Map + U

Highlight

Clear Highlighting

Digestion

Ladder

Edit…

List Enzymes

Quick Lists

Site Usage

Unique Sites

Absent Sites

Silent Sites

Text Map

ORFs


Find Next

Find Previous

Translate…

ORF Map

Selection Translate

Features


New Feature

List Features

Clear Features

Highlight Features

Feature Display Properties

Open Features File

Edit Feature Library

Tools


Find Primers…

Align Sequences…

BLAST Sequences at NCBI…

BLAST Sequences at wormbase…

Windows


Above the separator

Below the Separator

Help


Standard Genetic Code

AA Info

About ApE
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