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Introduction to Simvector

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Introduction to Simvector LAMP Designer 1.01 Manual PREMIER Biosoft International 3786 Corina Way, Palo Alto, CA 94303-4504 Tel: (650) 856-2703 FAX: (650) 618-1773 E-mail: [email protected] Copyright © 2011 by PREMIER Biosoft International. All Rights Reserved. Information in this manual may change without notice and does not represent a commitment on the part of PREMIER Biosoft International. The software described in this manual is provided by PREMIER Biosoft International under a License Agreement. The software may be used only in accordance with the terms of the agreement. PREMIER Biosoft International ("Premier") claims copyright to this program and documentation as an unpublished work. Claim of copyright does not imply waiver of Premier's other rights. This program and documentation are confidential and the property of Premier. Use, examination, reproduction, copying, decompilation, transfer, and/or disclosure to others are strictly prohibited except by express written agreement with Premier. For more information on PrimerPlex and product updates, visit the PREMIER Biosoft web site at http://www.PremierBiosoft.com. ii LAMP Designer 1.01 INTRODUCTION .................................................................................................. 1 Working Environment.....................................................................................................3 Main Window ...................................................................................................................8 LAMP Primer Search Parameters ................................................................................10 BLAST Search Parameters...........................................................................................12 View Cross Homology ..................................................................................................17 View Secondary Structures..........................................................................................19 Multiplex Results ........................................................................................................................20 TUTORIAL ......................................................................................................... 21 Open Project...............................................................................................................................21 Close Project ..............................................................................................................................21 Save Sequence As.....................................................................................................................21 Open Sequence from dbSNP.....................................................................................................22 Open Sequence From File .........................................................................................................22 Add Text Sequence....................................................................................................................23 Search Sequence ..........................................................................................................24 Set Parameters for BLAST search.............................................................................................25 Interpreting Cross Homology Results.........................................................................................30 LAMP Primer Search Results.....................................................................................................34 LAMP Primer Result Export: ........................................................................................35 Preferences....................................................................................................................36 Reaction Conditions ...................................................................................................................36 APPLICATION PREFERENCES ....................................................................... 37 TECHNICAL INFORMATION............................................................................. 38 Internet Setting..............................................................................................................38 Automatic Product Update...........................................................................................39 Standalone WWW BLAST for Linux ............................................................................40 Install RedHat Linux Server........................................................................................................40 Setup Firewall................................................................................................................41 Setup Apache webserver .............................................................................................42 Download BLAST Binaries...........................................................................................44 i LAMP Designer 1.01 Setup Standalone WWW BLAST Server......................................................................45 Download Databases .................................................................................................................46 Format Databases .........................................................................................................47 Database Formatting Tool..........................................................................................................47 Configuration Files .......................................................................................................49 Server configuration file and log file ...........................................................................................49 System Requirements ..................................................................................................50 Troubleshooting............................................................................................................51 Standalone WWW BLAST for Mac...............................................................................54 Download Blast Binaries for Mac ...............................................................................................54 Install Standalone www BLAST Server.......................................................................55 Set Up WWW BLAST Server For Mac..........................................................................56 Format Database For Mac ............................................................................................58 Database Formatting Tool..........................................................................................................58 Format Databases......................................................................................................................58 Configuration Files For Mac.........................................................................................60 Server configuration file and log file ...........................................................................................60 System Requirements For Mac....................................................................................61 Troubleshooting for Mac ..............................................................................................62 ALGORITHM AND FORMULAE........................................................................ 64 Formula for Melting Temperature Calculation............................................................................64 Formula for Calculating TaOpt.....................................................................................66 Formula for Free Energy ..............................................................................................67 Formula for Rating ........................................................................................................68 APPENDIX ......................................................................................................... 70 LAMP Primer Design Guidelines .................................................................................70 Glossary.........................................................................................................................71 SYSTEM REQUIREMENTS............................................................................... 73 TERMS OF USE................................................................................................. 74 ii LAMP Designer 1.01 Copyright .......................................................................................................................75 REFERENCES................................................................................................... 76 iii LAMP Designer 1.01 Introduction Welcome "LAMP" which stands for Loop-mediated Isothermal Amplification is a simple, rapid, specific and cost-effective nucleic acid amplification method solely developed by Eiken Chemical Co., Ltd. It amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. LAMP Designer designs a set of primers that recognizes six distinct regions in the DNA sequence. An inner primer containing the sequence of the sense and antisense strand of target DNA initiates LAMP. This is followed by strand displacement DNA synthesis primed by an outer primer and release of a single stranded DNA. This DNA now serves as a template for further amplification. LAMP Primer design: Designs optimal and highly specific primers by avoiding cross homologies found by
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