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

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eferences numbers, sequences, or user-defined feature labels is separated from the location by a forward slash. For a more detailed discussion of table entries and their standard typography, see http:// www.ncbi.nlm.nih.gov/collab/FT/index.html The table below contains a listing of the standard feature keys which have been implemented in Sequencher. Table 27-1 Feature keys groups and hierarchies Feature Specificity or detail Functional grouping A. misc_feature 1. misc_difference a) conflict b) unsure c) old_sequence d) variation e) modified_base f) mutation g) allele 2. gene 3. misc_signal a) promoter 1) CAAT_signal 2) TATA_signal 3) -35_signal 4) -10_signal 5) GC_signal b) RBS c) polyA_signal d) enhancer e) attenuator f) terminator g) rep_origin h) oriT Difference and change features Expression signal features 4. misc_RNA a) prim_transcript 1) precursor_RNA a) mRNA b) 5’clip c) 3’clip d) 5’UTR e) 3’UTR f) exon g) CDS 1) sig_peptide 2) transit_peptide 3) mat_peptide h) intron Transcript features SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 216
Feature Specificity or detail Functional grouping 5. Immunogobulin related a) C_region b) D_segment c) J_segment d) N_region e) S_region f) V_region g) V_segment 6. repeat_region a) repeat_unit b) LTR c) satellite d) transposon 7. misc_binding a) primer_bind b) protein_bind c) STS d) primer Repeat features Binding features 8. misc_recomb a) iDNA Recombination features 9. misc_structure a) stem_loop b) D-loop 10. gap 11. operon 12. source i) polyA_site j) rRNA k) tRNA l) scRNA m) snRNA n) snoRNA Structure features Feature table qualifiers Genbank Feature Qualifiers convey many different types of information. To accommodate this breadth there are several value formats: Qualifier Type Free text Table 27-2 Feature Qualifiers Description Free text qualifiers are usually descriptive phrases enclosed in double quotation marks. Controlled vocabulary or enumerated values Controlled vocabulary or enumerated values qualifiers are selections from a controlled vocabulary list and are entered without quotation marks. Examples of controlled vocabularies can be found in the Appendices to the GenBank Feature Table documentation (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. 217
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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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Page 186 and 187: Figure 19-1 Export Options dialog b
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Page 234 and 235: Qualifier type Description Citation
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