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

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Feature Key Default Feature Qualifier 5) GC_signal [gene] GC signal b) RBS [gene] RBS c) polyA_signal [gene] polyA signal d) enhancer [gene] enhancer ) attenuator [gene] attenuator f) terminator [gene] terminator g) rep_origin [gene] replication origin h) oriT [gene] oriT 4. misc_RNA [gene] misc RNA a) prim_transcript [gene] primary transcript 1) precursor_RNA [gene] precursor RNA a) mRNA [gene] mRNA b) 5’clip [gene] 5’clip c) 3’clip [gene] 3’clip d) 5’UTR [gene] 5’UTR e) 3’UTR [gene] 3’UTR f) exon [gene] exon g) CDS [gene] CDS 1) sig_peptide [gene] signal peptide 2) transit_peptide [gene] transit peptide 3) mat_peptide [gene] mature peptide h) intron [gene] intron i) polyA_site [gene] polyA site j) rRNA [gene] rRNA k) tRNA [gene] tRNA l) scRNA [gene] scRNA m) snRNA [gene] snRNA n) snoRNA [gene] snoRNA 5. Immunogobulin related Immunogobulin related a) C_region [gene] C region b) D_segment [gene] D segment c) J_segment [gene] J segment d) N_region [gene] N region e) S_region [gene] S region f) V_region [gene] V region g) V_segment [gene] V segment SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 220
Feature Key Default Feature Qualifier 6. repeat_region [gene] [rpt_type] repeat region [rpt_family] a) repeat_unit [gene] [rpt_type] repeat unit b) LTR [gene] LTR c) satellite [gene] [rpt_type] satellite Transposon ** transposon 7. misc_binding misc binding of [bound_moiety] a) primer_bind [gene] primer binding site b) STS STS [locus_tag] c) protein_bind [bound_moiety] protein binding site Primer** primer 8. misc_recomb Misc recombination [gene] [map] a) iDNA [gene] iDNA 9. misc_structure misc structure [note] a) stem_loop [gene] stem loop b) D-loop [gene] D-loop 10. gap gap of [estimated_length] 11. operon [operon] operon Source [organism] Unrecognized *** * Sequencher Feature Key is for personal annotation ** Legacy keys *** This is used for Feature Keys which are unknown to Sequencher so that they can be imported in to a project SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 221
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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
Page 192 and 193: [Project Name] and [User Name]. You
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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 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
Page 222 and 223: You may require a more complex deli
Page 226 and 227: Code Base(s) Meaning 5 A or Another
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 240 and 241: Name CursorProject Window Dialog bo
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