Macvector 12.6 User Guide2.Pdf
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MacVector 12.6 MacVector User Guide 1 2 MacVector User Guide Copyright statement Copyright MacVector, Inc, 2012. 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 Text view....................................................................................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...........................................................35 Overview....................................................................................35 Performing sequence analysis....................................................36 Viewing results...........................................................................37 Magnifying a graphic area......................................................37 Outputting results.......................................................................38 Saving graphics .....................................................................38 Formatting the Aligned Sequence view .....................................41 Formatting the aligned sequence .............................................42 Displaying a score line ...........................................................43 Displaying a query line...........................................................44 Configuring the numeric keypad................................................45 Using the proofreader.................................................................46 Reading a typed sequence .......................................................46 Proofreading a sequence.........................................................46 Searching....................................................................................47 Searching sequences...............................................................47 Searching features..................................................................50 MacVector User Guide 5 Searching results....................................................................51 4 Working with MacVector Files.....................................53 Overview....................................................................................53 MacVector file types ..................................................................54 Sequence files ........................................................................54 Enzyme files ..........................................................................54 Subsequence files ...................................................................54 Scoring matrix files ................................................................55 Codon bias files .....................................................................55 Multiple alignment files ..........................................................55 Managing files............................................................................56 Creating new files ..................................................................56 Opening files .........................................................................56 Saving files............................................................................58 Closing files ..........................................................................58 Enzyme files...............................................................................58 Selecting enzymes for site analysis...........................................59 Adding entries to an enzyme file ..............................................60 Copying entries between enzyme files.......................................61 Editing entries in an enzyme file ..............................................62 Deleting entries from an enzyme file ........................................62 Subsequence files.......................................................................63 Selecting subsequences for searches ........................................64 Adding entries to a subsequence file ........................................65 Copying entries between subsequence files...............................67 Editing entries in a subsequence file ........................................67 Deleting entries from a subsequence file...................................68 Scoring matrix files....................................................................68 Editing match and mismatch scores .........................................69 Editing hash codes .................................................................70 Editing tweak values...............................................................71 Sequence files ............................................................................72 5 Working with Sequences and Features .....................75 Overview....................................................................................75 Sequence window ......................................................................76 Managing sequences ..................................................................76 Opening a sequence ...............................................................76 Creating a new sequence ........................................................77 6 MacVector User Guide Saving a sequence..................................................................77 Exporting view-specific data ...................................................80 Printing a sequence................................................................80 Closing a sequence.................................................................82 Editor view.................................................................................82 Selecting residues...................................................................87 Adding residues .....................................................................89 Deleting residues ...................................................................90 Reversing a sequence .............................................................91 Complementing a sequence.....................................................91 Reversing and complementing a sequence ................................91 Map view....................................................................................92 Formatting the Map view........................................................93 Features view ...........................................................................113 Feature keywords.................................................................115 Adding a feature ..................................................................115 Editing a feature ..................................................................118 Deleting a feature ................................................................118 Sorting features....................................................................118 Annotations view .....................................................................119 Types of annotation ..............................................................120