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	Tehdyt toimenpiteet Pregap4 - Table of Contents Pregap4 Organisation of the Pregap4 Manual Introduction Summary of the Files used and the Processing Steps Introduction to the Pregap4 User Interface Introduction to the Files to Process Window Introduction to the Configure Modules Window Introduction to the Textual Output Window Introduction to Running Pregap4 Pregap4 Menus Pregap4 File menu Pregap4 Modules menu Pregap4 Information source menu Pregap4 Options menu Specifying Files to Process Running Pregap4 Non Interactive Processing Command Line Arguments Configuring the Pregap4 User Interface Fonts and Colours Window Styles Configuring Modules General Configuration Estimate Base Accuracies Phred ATQA Trace Format Conversion Compress Trace Files Initialise Experiment Files Augment Experiment Files Quality Clip Sequencing Vector Clip Cross_match Cloning Vector Clip Screen for Unclipped Vector Screen Sequences Blast Screen Interactive Clipping Extract Sequence RepeatMasker Tag Repeats Mutation Detection Reference Traces and Reference Sequences Trace Difference Mutation Scanner Gap4 Shotgun Assembly Cap2 Assembly Cap3 Assembly FakII Assembly Phrap Assembly Enter Assembly into Gap4 Email Old Cloning Vector Clip - Obsolete ALF/ABI to SCF Conversion - Obsolete Using Config Files Pregap4 Naming Schemes Mutation Detection Naming Scheme Old Sanger Centre Naming Scheme New Sanger Centre Naming Scheme Writing Your Own Naming Schemes Pregap4 Components Information Sources Simple Text Database Experiment File Line Types Adding and Removing Modules Low Level Pregap4 Configuration Low Level Global Configuration Low Level Component Configuration Low Level Module Configuration General Configuration ALF/ABI to SCF Conversion Estimate Base Accuracies Phred ATQA Compress Trace Files Trace Format Conversion Initialise Experiment Files Augment Experiment Files Uncalled Base Clip Quality Clip Sequencing Vector Clip Cross_match Cloning Vector Clip Old Cloning Vector Clip Screen for Unclipped Vector Screen Sequences Blast Screen Interactive Clipping Extract Sequence Tag Repeats RepeatMasker Mutation Detection Gap4 Shotgun Assembly Cap2 Assembly Cap3 Assembly FakII Assembly Phrap Assembly Enter Assembly into Gap4 Email Shutdown Writing New Modules An Overview of a Module Functions Module Variables Global Variables Builtin Functions An Example Module General Index File Index Variable Index Function Index This document was generated on 25 April 2003 using the texi2html translator version 1.39 (with local modifications) This page is maintained by staden-package. Last generated on 25 April 2003. URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_unix_98.html