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

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Qualifier type Description Citation or reference numbers Sequences Feature labels A citation or reference number is enclosed in square brackets to distinguish it from other numbers. Since 1998, it has not been acceptable to use a literal sequence of bases as the Sequence Qualifier. The feature label qualifier supports clarity in reporting by making sure your references are unambiguous. An example of a feature label would be alcA (see example below). The figure below shows a typical example of a feature table entry with qualifiers. In this example the feature key is CDS. The location is expressed as two numbers. The qualifiers tell the reader that the gene is alcA, the product of the gene is alcohol dehydrogenase and that the evidence is experimental. Figure 27-2 Qualifier examples Key Location/Qualifiers CDS 6006..>6253 /gene=”alcA” /experiment=”experimental evidence, no additional details recorded” /note=”ADHI; ethanol regulon” /codon_start=1 /product=”alcohol dehydrogenase I” Information on the Feature Keys and Tables and Qualifiers has been taken from the official GenBank documentation which can be obtained from the following URL http:// www.ncbi.nlm.nih.gov/collab/FT/index.html SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 218
29. Appendix - Default Feature Qualifiers In this table you will find the default Feature Qualifier for each Feature Key as implemented in Sequencher. Feature Key Default Feature Qualifier Sequencher * A. misc_feature misc feature [note] 1. misc_difference misc difference [note] a) conflict conflict [compare] b) unsure unsure difference c) old_sequence old sequence [compare] d) variation variation [note] e) modified_base [gene] modified base [mod_base] Allele ** allele Mutation ** mutation 2. gene [gene] gene 3. misc_signal [gene] misc signal a) promoter [gene] promoter 1) CAAT_signal [gene] CAAT signal 2) TATA_signal [gene] TATA signal 3) -35_signal [gene] -35 signal 4) -10_signal [gene] -10 signal SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 219
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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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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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Page 186 and 187: Figure 19-1 Export Options dialog b
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Page 190 and 191: Figure 19-3 Copy As Protein Transla
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Page 198 and 199: Choosing a genetic code You will fi
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Page 210 and 211: Variance Table The Variance Table p
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Page 216 and 217: Figure 22-3 The Circular Genome Siz
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Page 228 and 229: Feature Display Color Style Second
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Page 236 and 237: Feature Key Default Feature Qualifi
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