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

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THIS IS AN AGREEMENT BETWEEN YOU, THE END USER, AND US, GENE CODES. BY OPENING THE SEALED DISK PACKAGE, YOU ARE AGREEING TO BE BOUND BY THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE TO THESE TERMS, PROMPTLY RETURN THE UNOPENED DISK PACKAGE AND ALL ACCOMPANYING MATERIALS TO US OR TO YOUR DEALER FOR A REFUND. License. We grant you the right to use the enclosed software program (the Software) on a single terminal connected to a single computer. The Software is accompanied by a hardware-locking device that prevents its full use on any computer without the device; if the Software is used without the locking device, it operates in demonstration mode only. You may not use the Software on a network without obtaining a license for each terminal on which the Software will be used. You may not use the Software for any purpose related to the use, development, analysis, testing, or research on biological weapons. Copyright. The Software is protected by United States copyright laws and international treaty provisions. You must treat the Software like any other copyrighted material, such as a book or musical recording. You may, however, either (a) make copies of the Software for backup or archival purposes; (b) transfer the Software to a single hard disk, provided you keep the original; or (c) make copies of the Software to give to others for purposes of demonstrating the Software. You may not copy any written materials accompanying the Software. Other restrictions. You may not rent or lease the Software, but you may transfer it and the accompanying written materials on a permanent basis provided you retain no copies and the recipient agrees to the terms of this agreement. You may not reverse engineer, decompile, or disassemble the Software. Limited Warranty. We warrant that the Software will perform substantially in accordance with the accompanying written materials for a period of 90 days from the date of receipt. Any implied warranties on the Software are limited to 90 days. Some states do not allow limitations on duration of an implied warranty, so this limitation may not apply to you. Remedies. Our entire liability and your exclusive remedy shall be, at our option, either (a) return of the price paid or (b) repair or replacement of the Software that does not meet our limited warranty and that is returned to us. Our limited warranty is void if failure of the Software has resulted from abuse or misapplication. We warrant the replacement Software under this limited warranty for the remainder of the original warranty period or 30 days, whichever is longer. NO OTHER WARRANTIES. WE DISCLAIM ALL OTHER EXPRESS OR IMPLIED WARRANTIES, INCLUDING THE IMPLIED WARRANTIES OF THE MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. OUR LIMITED WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS. YOU MAY HAVE OTHER RIGHTS, WHICH VARY FROM STATE TO STATE. NO LIABILITY FOR CONSEQUENTIAL DAMAGES. IN NO EVENT SHALL WE BE LIABLE FOR ANY DAMAGES WHATEVER, INCLUDING LOSS OF PROFITS, ARISING OUT OF THE USE OR INABILITY TO USE THIS SOFTWARE, EVEN IF WE HAVE BEEN ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES. BECAUSE SOME STATES DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR CONSEQUENTIAL OR INCIDENTAL DAMAGES, THIS LIMITATION MAY NOT APPLY TO YOU. U.S. Government Rights. The Software and documentation are provided with RESTRICTED RIGHTS. Use of duplication, or disclosure by the Government is subject to restrictions set forth in subparagraph (c) (1) (ii) of the Rights in Technical Data and Computer Software clause at 52.227.7013. The contractor/ manufacturer manufacturer is Gene Codes Corporation, Ann Arbor, Michigan. i
Sequencher 4.8 User Manual The complete software solution for sequencing DNA Windows Gene Codes Corporation
Page 4 and 5: © 1991 - 2007 Gene Codes Corporati
Page 6 and 7: Templates .........................
Page 8 and 9: Set Circular Genome Size ..........
Page 10 and 11: The Bases View ....................
Page 12 and 13: Protein translations for the Consen
Page 14 and 15: Setting header, footer and margin o
Page 16 and 17: Page Intentionally Left Blank xv
Page 18 and 19: We welcome your comments or support
Page 20 and 21: Navigating Sequencher Help The Sequ
Page 22 and 23: Contig menu The commands in the Con
Page 24 and 25: Page Intentionally Left Blank SEQUE
Page 26 and 27: Figure 3-1 An empty Sequencher Proj
Page 28 and 29: Figure 3-4 Project Window with Larg
Page 30 and 31: value in the Confidence pane of the
Page 32 and 33: Editing the information for a seque
Page 34 and 35: Page Intentionally Left Blank SEQUE
Page 36 and 37: How to import using menu commands I
Page 38 and 39: Figure 4-2 Browse for Folder dialog
Page 40 and 41: Importing Confidence Scores Many ba
Page 42 and 43: If you have finished working with S
Page 44 and 45: Selecting sequences Selecting seque
Page 46 and 47: Renaming a sequence or contig Renam
Page 48 and 49: Closing the Project Window When you
Page 50 and 51: 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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Page Intentionally Left Blank SEQUE
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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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Figure 19-3 Copy As Protein Transla
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[Project Name] and [User Name]. You
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Colors as Backgrounds Sometimes, di
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Choosing a genetic code You will fi
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time you select the Review button f
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Label & Name The Label & Name prefe
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Click the Use Blank Project radio b
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Use the Columns For Multiple Traces
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If you are making changes to the wa
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Variance Table The Variance Table p
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Figure 22-1 The Validate mtDNA Prof
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Figure 22-3 The Circular Genome Siz
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Menu/Window Command Windows Select
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You may require a more complex deli
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Code Base(s) Meaning 5 A or Another
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Feature Display Color Style Second
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eferences numbers, sequences, or us
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Qualifier type Description Citation
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Feature Key Default Feature Qualifi
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Name CursorProject Window Dialog bo
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