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Macvector 11 2 Macvector User Guide Copyright Statement MacVector 11 2 MacVector User Guide Copyright statement Copyright MacVector, Inc, 2009. 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. Trademarks Gateway®, TOPO®, Vector NTI® and Zero Blunt® are regiestered trademarks of Life Technologies, Carlsbad, California, USA. Vector NTI Advance™ is a trademark of Life Technologies, Carlsbad, California, USA. 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 Starting Point dialog ..............................................................24 Sequence window ......................................................................24 Editing sequence data.............................................................25 Sequence maps ......................................................................25 Features and annotations........................................................26 The Text Sequence window .......................................................27 Analysis toolbar .........................................................................28 Site and motif searches ..............................................................28 Sequence comparison, alignment and phylogeny......................29 Aligning sequences to a reference .............................................29 Protein and nucleic acid toolbox analysis ..................................30 3 General Procedures...........................................................33 Overview....................................................................................33 Performing sequence analysis....................................................34 Viewing results...........................................................................35 Magnifying a graphic area......................................................35 Outputting results.......................................................................36 Saving graphics .....................................................................36 Formatting the text sequence display.........................................39 Formatting residue sequences .................................................40 Formatting features................................................................41 Formatting the aligned sequence display ...................................42 Formatting the aligned sequence .............................................44 Displaying a score line ...........................................................45 Displaying a query line...........................................................45 Formatting the map display........................................................46 Editing the global symbol set...................................................47 Editing the sequence symbol set...............................................57 Editing the general map appearance........................................59 MacVector User Guide 5 Printing maps ........................................................................62 Configuring the numeric keypad................................................64 4 Working with MacVector Files.....................................65 Overview....................................................................................65 MacVector file types ..................................................................66 Sequence files ........................................................................66 Enzyme files ..........................................................................66 Subsequence files ...................................................................66 Scoring matrix files ................................................................67 Codon bias files .....................................................................67 Multiple alignment files ..........................................................67 Managing files............................................................................68 Creating new files ..................................................................68 Opening files .........................................................................68 Saving files............................................................................70 Closing files ..........................................................................70 Enzyme files...............................................................................70 Selecting enzymes for site analysis...........................................71 Adding entries to an enzyme file ..............................................72 Copying entries between enzyme files.......................................73 Editing entries in an enzyme file ..............................................74 Deleting entries from an enzyme file ........................................74 Subsequence files.......................................................................75 Selecting subsequences for searches ........................................76 Adding entries to a subsequence file ........................................77 Copying entries between subsequence files...............................79 Editing entries in a subsequence file ........................................80 Deleting entries from a subsequence file...................................80 Scoring matrix files....................................................................81 Editing match and mismatch scores .........................................81 Editing hash codes .................................................................82 Editing tweak values...............................................................83 Sequence files ............................................................................84 5 Working with Sequences .................................................87 Overview....................................................................................87 The Sequence window ...............................................................88 Managing sequences ..................................................................88 Opening a sequence ...............................................................88 6 MacVector User Guide Creating a new sequence ........................................................89 Saving a sequence..................................................................89 Exporting view-specific data ...................................................92 Printing a sequence................................................................93 Closing a sequence.................................................................94 The Editor view..........................................................................94 Selecting residues...................................................................99 Adding residues ...................................................................101 Deleting residues .................................................................101 Reversing a sequence ...........................................................102 Complementing a sequence...................................................102 Reversing and complementing a sequence ..............................103 The Map view ..........................................................................103 The Features view ....................................................................104 Feature keywords.................................................................106 Adding a feature ..................................................................106 Editing a feature ..................................................................109 Deleting a feature ................................................................109 Sorting features....................................................................109 Using auto-annotation to add features and feature appearance information...............................................................................110 How auto-annotation works ..................................................110 Limitations
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