Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

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Name CursorProject Window Dialog box Delimiter Double-click Drag Elevator button Enzyme Exemplar Field Handle Hierarchical menu Modal dialog box Motif Mouse MSF NEXUS/Paup Definition The indicator on a computer screen that shows the currently active location. Cursors have various shapes, indicating different purposes and capabilities. Any of several special windows that the operating system or Sequencher displays when it needs to alert you to something you need to know, or needs to ask you a question. Usually a character such as / or - which separates elements of a sequence name. Click twice in quick succession. You can set the amount of time you have before the machine decides that you have performed a second single click rather than a double-click. Press the mouse button and hold it down while you move the mouse (and thus the cursor) across the screen. A very small scroller that allows you to increase or decrease a numerical value by using the mouse. An elevator button has an up arrow and a down arrow. In this manual, enzyme always refers to a restriction endonuclease. Chosen or primary sequence. Literal meaning typical example or excellent model. A rectangle in which the user can (or in some cases must) enter names or other information. The portion of a sequence name between two consecutive delimiters. Also known as Assembly handle. A hidden menu that looks like a command until you invoke it. When you move the cursor over the name of the hierarchical menu, it appears to the right of the parent menu. A hierarchical menu is indicated by a right-pointing triangle. A dialog box that requires a response before you can continue with regular actions in the application. In Sequencher this is a short subsequence of 50 bases or less. The mouse is integral to the interface. It controls the position of the cursor on the screen and is used to enter some kinds of information. (See Click, Double-click, Drag). Multiple Sequence Format. A format used by multiple sequence alignment programs. Format used by phylogentic and cladistic software. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 224
Name Project Project window Quality score Radio button Reference sequence Refrigerator SCF Secondary peak Sequence Sequence Editor Slider Title bar VecBase Definition A project contains sequences, information on how these sequences fit together to form larger pieces and parameter information, specified by the user, that controls alignment operations. The window in which Sequencher displays the contigs and unincorporated Sequences of a project. Items in the Project Window are can be shown as icons, small icons or as a sorted list. A number associated with each base call and which defines the likelihood that a base call is incorrect. See also Confidence score. A control that lets you choose among alternate possibilities. Radio buttons always appear in sets of at least two. Click one of the buttons to select it. A button that is selected is shown with a filled circle; buttons that are not selected are shown with open circles. A sequence used as a prototype or benchmark sequences. If a sequence has been designated as Reference within Sequencher it has special properties. A special folder in which to store subsets of sequences which need to remain in your project. Standard Chromatogram Format. A format used to store analyzed data or fragment data for a single sample. A chromatogram peak whose height may be less than that of the primary peak and whose presence may indicate that a heterozygote exists at that position. A small piece of DNA, decoded into its component bases, in order, represented as text. Sometimes in reverse order, depending upon the vagaries of the sequencing procedure. The window used for editing DNA sequences. This editor looks much like a word processor and supports the standard text editing commands: Cut, Copy, Paste and Undo. An on screen control that simulates the action of a slide control that might normally be used as a volume or dimmer control on a household appliance. The region at the top of a window on the computer. A cloning vector sequence database prepared by Friedhelm Pfeiffer, in collaboration with William Gilbert. Also a file with this name, in VecBase (CODATA) format, Part of the Sequencher distribution. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 225
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THIS IS AN AGREEMENT BETWEEN YOU, T
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© 1991 - 2007 Gene Codes Corporati
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Templates .........................
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Set Circular Genome Size ..........
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The Bases View ....................
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Protein translations for the Consen
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Setting header, footer and margin o
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We welcome your comments or support
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Navigating Sequencher Help The Sequ
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Contig menu The commands in the Con
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Page Intentionally Left Blank SEQUE
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Figure 3-1 An empty Sequencher Proj
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Figure 3-4 Project Window with Larg
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value in the Confidence pane of the
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Editing the information for a seque
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How to import using menu commands I
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Figure 4-2 Browse for Folder dialog
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Importing Confidence Scores Many ba
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If you have finished working with S
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Selecting sequences Selecting seque
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Renaming a sequence or contig Renam
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Closing the Project Window When you
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Performing a trim with default sett
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additional control within the Trim
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Figure 6-7 The polylinker window No
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Setting Vector Trimming Criteria Se
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Basic Reference Sequence properties
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When the To Reference by Name comma
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A locked editor is read-only. You c
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If your sequence was called “MyPU
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Viewing summary information in the
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Figure 8-7 ORF selected by Next Met
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If you want to assign a personal an
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Voice verification Sequencher provi
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Chapter 9 “Sequence Assembly” f
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Figure 9-2 The Clean Data algorithm
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Performing the assembly Automatic a
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Figure 9-5 Interactive assembly sho
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The new contig will appear in the P
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When you use a Name Delimiter, it w
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If the Expression is a delimiter bo
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Figure 10-6 The Project Window with
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it is in the reverse orientation. T
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Figure 11-2 Contig overview Fifure
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Base Numbers At Transitions Clickin
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Label Name Function E F G H Sequenc
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Consensus to Forensic Standards In
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consensus is from a base with a low
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move the gaps to the 5’ end, sele
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Figure 12-4 Fill Void dialog box De
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First select the base or range of b
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The Translated Variance Table If yo
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Structure of the Translated Varianc
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(see Figure 13-5). It is possible f
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Figure 13-7 Translated Variance Tab
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If you want to restrict the Compari
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Figure 13-13 Creating a Joined feat
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In either case, the method you choo
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You can edit your data directly in
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Figure 13-17 The Translated Varianc
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Figure 13-19 Extract from Variance
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The Population Table lists the vari
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If you want to remove sample sequen
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Select Individual Variance Reports
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If you prefer to copy your Translat
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You can copy your Translated Varian
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Summary report display options Sequ
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Enabling the protein display To ena
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Note: Remember that even if a seque
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If you select the Contig Chromatogr
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Select command Table 15-1 Summary o
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Note: The Extend Selection command
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Figure 16-2 Restriction map options
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example, if you were displaying onl
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Figure 16-8 Checkmarked enzyme list
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display this view by going to the V
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The default setting shows exact mat
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Creating and editing features To cr
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Quick feature creation To create a
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Figure 18-1 A dimmed icon Finding t
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Note: If you pause between characte
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a dialog box (Figure 18-6). This le
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Figure 19-1 Export Options dialog b
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You should remember to provide a re
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Page 196 and 197: Colors as Backgrounds Sometimes, di
Page 198 and 199: Choosing a genetic code You will fi
Page 200 and 201: time you select the Review button f
Page 202 and 203: Label & Name The Label & Name prefe
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Page 210 and 211: Variance Table The Variance Table p
Page 214 and 215: Figure 22-1 The Validate mtDNA Prof
Page 216 and 217: Figure 22-3 The Circular Genome Siz
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Page 228 and 229: Feature Display Color Style Second
Page 232 and 233: eferences numbers, sequences, or us
Page 234 and 235: Qualifier type Description Citation
Page 236 and 237: Feature Key Default Feature Qualifi
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