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Index

Introduction

Single Sequence Files
Single Sequence editor Setting origins
Map View Show/Hide graphics palette
Editing the general map appearance
Features
Editing Features
Sorting Features
Annotations
Types of annotation
Editing annotations

Chromatogram Files
Chromatogram editor
Saving edited Chromatograms

Multiple Sequence Files
Opening multiple sequence files
The MSA Editor
Setting MSA Editor display options
Calculating a consensus line
Displaying a consensus line
Working with color groups
Editing alignments
Adding and selecting sequences
Changing and deleting sequences
Ordering and naming sequences
Displaying multiple alignments
Multiple alignment text display
Pairwise alignment text display
Multiple alignment picture display
Consensus sequence display
Saving multiple sequence alignments

Support Files
Codon bias files
Enzyme files
Selecting enzymes
Editing enzyme files
Scoring matrix file
Match and mismatch scores
Hash codes
Tweak values
Subsequence files
Selecting subsequences
Editing subsequence files

File Menus
New
Open
Close
Save
Save As
Page Setup

Edit Menus
Undo
Cut
Copy
Paste
Delete
Select all
Add new sequence
Add sequences from file
Delete sequence
Reverse
Complement
Reverse & Complement
Find
Jump to

MacVector Preferences and the Options menu
Format annotated display
Graphical Output Options Format aligned display
Symbol editor
Feature panel
Result panel
Title panel
Ruler panel
Sequence panel
Segment map panel
Modify genetic codes
Selecting genetic codes
Editing genetic codes

Analyze Menus
Restriction enzyme
Searching for restriction sites
Filtering restriction site results
Displaying restriction site results
Automatic Restriction Enzyme Analysis
Nucleic acid subsequence
Searching for subsequences
Filtering subsequences results
Displaying subsequence results
Open reading frames
Nucleic Acid Analysis Toolbox
Nucleic Acid Analysis Toolbox results window
Base composition
Base composition plots
Nucleotide frequency histograms
Primers
Design Primers (Primer3)
PCR primer pairs
Test PCR primer pair
Sequencing primers/probes
Test sequencing primer/probe
Translating DNA to protein
Generating a transcript
Translating DNA or mRNA to protein
Reverse translation
Proteolytic enzyme
Searching for proteolytic sites
Filtering proteolytic site results
Displaying proteolytic site results
Protein subsequence
Searching for protein motifs
Filtering motif results
Displaying motif results
Protein analysis toolbox
Pustell DNA matrix
Performing a DNA matrix analysis
Displaying DNA matrix results
Pustell protein matrix
Performing a protein matrix analysis
Displaying matrix results
Pustell protein/DNA matrix
Performing a matrix analysis
Displaying matrix results
ClustalW
Performing a ClustalW alignment
Displaying a ClustalW alignment
Guide tree
Reconstructing phylogenies
Position masking
Generating phylogenetic trees
Viewing and editing trees
The tree viewer window
Editing trees
Setting the tree display options
Sorting MSAs top match trees
Saving and printing trees
Align to Reference
The main window
Assembling sequences

SNP Report
Editing assemblies
Saving assemblies

Database Menus
Align to folder
Aligning sequences in a folder
Displaying alignment results
Online search for Similar Sequences (Blast)
Using BLAST searches
Displaying BLAST search results
Retrieving matching sequences
Retrieve and Open
Retrieve to disk
Online Keyword Search for Sequences (Entrez)
Searching the Entrez database
Browsing the Entrez search results
Retrieving information from Entrez

Windows Menus
Show Job Manager
Show proofreader
Show/Hide graphics palette
Editing the sequence symbol set
Editing the general map appearance
IUPAC key
Stack
Tile
Full titles

Keyboard Shortcuts
General
Plot result windows
MSA editor

Assembler
The project window
Assembling sequences
Base calling
Vector trimming
Assembling
Editing assemblies
Saving assemblies