Macvector 10.6 2 Macvector User Guide Copyright Statement

MacVector 10.6 2 MacVector User Guide Copyright statement Copyright MacVector, Inc, 2008. All rights reserved. This document contains proprietary information of MacVector, Inc and its licensors. It is their exclusive property. It may not be reproduced or transmitted, in whole or in part, without written agreement from MacVector, Inc. The software described in this document is furnished under a license agreement, a copy of which is packaged with the software. The software may not be used or copied except as provided in the license agreement. MacVector, Inc reserves the right to make changes, without notice, both to this publication and to the product it describes. Information concerning products not manufactured or distributed by MacVector, Inc is provided without warranty or representation of any kind, and MacVector, Inc will not be liable for any damages. MacVector User Guide 3 4 MacVector User Guide 1 Introduction to the User Guide ....................................19 Overview....................................................................................19 The MacVector documentation set.............................................20 About this user guide..............................................................20 Conventions in this user guide...................................................20 Interface conventions .............................................................21 Navigation aids ..........................................................................21 2 Introduction to MacVector.............................................23 Overview....................................................................................23 MacVector sequence files...........................................................24 The Sequence window ...............................................................24 Editing sequence data.............................................................24 Sequence maps ......................................................................24 Features and annotations........................................................25 The Annotated Sequence window..............................................26 Site and motif searches ..............................................................26 Sequence comparison, alignment and phylogeny......................27 Protein and nucleic acid toolbox analysis ..................................28 3 General Procedures...........................................................31 Overview....................................................................................31 Viewing results...........................................................................32 Magnifying a graphic area......................................................32 Outputting results.......................................................................32 Saving graphics .....................................................................33 Formatting the annotated sequence display ...............................35 Formatting residue sequences .................................................36 Formatting features................................................................37 Formatting the aligned sequence display ...................................38 Formatting the aligned sequence .............................................39 Displaying a score line ...........................................................41 Displaying a query line...........................................................41 Formatting the map display........................................................42 Editing the global symbol set...................................................43 Editing the sequence symbol set...............................................53 Editing the general map appearance........................................56 Printing maps ........................................................................59 Configuring the numeric keypad................................................60 4 Working with MacVector Files.....................................63 Overview....................................................................................63 MacVector User Guide 5 MacVector file types ..................................................................64 Sequence files ........................................................................64 Enzyme files ..........................................................................64 Subsequence files ...................................................................64 Scoring matrix files ................................................................65 Codon bias files .....................................................................65 Multiple alignment files ..........................................................65 Managing files............................................................................66 Creating new files ..................................................................66 Opening files .........................................................................66 Saving files............................................................................68 Closing files ..........................................................................68 Enzyme files...............................................................................68 Selecting enzymes for site analysis...........................................69 Adding entries to an enzyme file ..............................................70 Copying entries between enzyme files.......................................71 Editing entries in an enzyme file ..............................................72 Deleting entries from an enzyme file ........................................72 Subsequence files.......................................................................73 Selecting subsequences for searches ........................................74 Adding entries to a subsequence file ........................................75 Copying entries between subsequence files...............................77 Editing entries in a subsequence file ........................................77 Deleting entries from a subsequence file...................................78 Scoring matrix files....................................................................78 Editing match and mismatch scores .........................................79 Editing hash codes .................................................................80 Editing tweak values...............................................................81 Sequence files ............................................................................82 5 Working with Sequences .................................................85 Overview....................................................................................85 The Sequence window ...............................................................86 Managing sequences ..................................................................86 Opening a sequence ...............................................................87 Creating a new sequence ........................................................88 Saving a sequence..................................................................88 Printing a sequence................................................................90 Closing a sequence.................................................................91 6 MacVector User Guide The Editor view..........................................................................92 Selecting residues...................................................................95 Adding residues .....................................................................96 Deleting residues ...................................................................97 Reversing a sequence .............................................................98 Complementing a sequence.....................................................98 Reversing and complementing a sequence ................................98 The Map view ............................................................................98 The Features view ......................................................................99 Feature keywords...................................................................99 Adding a feature ..................................................................100 Editing a feature ..................................................................103 Deleting a feature ................................................................103 Sorting features....................................................................103 The Annotations view ..............................................................104 Types of annotation ..............................................................104 Adding an annotation ...........................................................107 Editing an annotation...........................................................107 Deleting an annotation .........................................................107 Using the proofreader...............................................................107 Reading a typed sequence .....................................................108 Proofreading a sequence.......................................................108 Searching..................................................................................109 Searching sequences.............................................................109 Searching features................................................................112

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