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

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You should remember to provide a relevant name to define the new project, because you have derived it from a selection of multiple items. Note: Unlike other Export commands which may create a number of files on your hard disk, this command will create only one new project. Export Selected Bases You may want to export selected bases rather than an entire sequence. To do so, drag the mouse to highlight your selected bases or go to the Select menu and use the Bases by Number command. Then go to the File menu and choose Export and click on Selected Bases… from the submenu. You will then see the Save As window, which allows you to choose your format options and preferred location. Export Options If you click the Options button in an export dialog box, Sequencher provides a context sensitive dialog box for changing the export options. Select the options you want and click Export. Export Formats When you export a file, you may want to specify a file format so other software can access it. Click the Format: dropdown menu in the export dialog box. The menu will display a list of the available formats. The Sequencher Export menu is context sensitive, which means that it varies based on whether your selection contains a sequence, a contig or both. For each kind of export, you will be prompted to apply appropriate formats. See Table below for more information. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 172
Table 19-1 Examples of Sequencher’s Export formats Sequence & Consensus formats Export format type ASCII plain, Unformatted, AFDIL, Fitch, Genentech, IG, Strider GenBank, NBRF, EMBL FASTA, FASTA concatenated GCG Nexus/PAUP interleaved, Nexus/ PAUP sequential, Phylip, Phylip 3, Phylip4 SCF 2.0, SCF 3.0 Description Plain text Specialist and legacy formats Database formats Commonly used formats Phylogenetic program format Standard Chromatogram Format Contig formats CAF Common Assembly Format MSF FASTA aligned Nexus/Paup Multiple Sequence Format Phylogenetic program format Phylogenetic program format Subproject formats CAF Common Assembly Format FASTA Sequencher Commonly used formats Older project file formats Note: SCF - Standard Chromatogram File format is a file format for exchanging data between different sequencing systems that use four color chromatograms to show sequencing data. Most current sequencing hardware supports this file standard. Exporting protein translations Sequencher can automatically translate bases into proteins as it copies items to the clipboard. These protein sequences can then be exported to another file or program. To perform this, select a portion or all of the sequence and then go to the Edit menu and choose Copy As and Protein Translation… from the submenu. Sequencher asks you whether you want to translate only the selected bases or whether you want the entire sequence but in a specific frame. The default setting is to translate only the bases you selected. You can then take this copy and paste it into another program as you would any other information. SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 173
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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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Page 146 and 147: You can copy your Translated Varian
Page 148 and 149: Summary report display options Sequ
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Page 160 and 161: Note: The Extend Selection command
Page 162 and 163: Figure 16-2 Restriction map options
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Page 166 and 167: Figure 16-8 Checkmarked enzyme list
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Page 172 and 173: Creating and editing features To cr
Page 174 and 175: Quick feature creation To create a
Page 178 and 179: Figure 18-1 A dimmed icon Finding t
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Page 186 and 187: Figure 19-1 Export Options dialog b
Page 190 and 191: Figure 19-3 Copy As Protein Transla
Page 192 and 193: [Project Name] and [User Name]. You
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Page 198 and 199: Choosing a genetic code You will fi
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Page 202 and 203: Label & Name The Label & Name prefe
Page 204 and 205: Click the Use Blank Project radio b
Page 206 and 207: Use the Columns For Multiple Traces
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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
Page 220 and 221: Menu/Window Command Windows Select
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Page 226 and 227: Code Base(s) Meaning 5 A or Another
Page 228 and 229: Feature Display Color Style Second
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Page 234 and 235: Qualifier type Description Citation
Page 236 and 237: Feature Key Default Feature Qualifi
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Name CursorProject Window Dialog bo
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