Gap4 Menus

The main window for gap4 contains File, Edit, View, Options, Experiments, Lists and Assembly menus.

Gap4 File menu

The File menu includes database opening and copying functions and consensus calculation options.

• Change Directory ( see section Directories)
• Check Database ( see section Check Database)
• New ( see section Opening a New Database)
• Open ( see section Opening an Existing Database)
• Copy Database ( see section Making Backups of Databases)
• Copy Readings ( see section Copying Readings)
• Save Consensus ( see section The Consensus Calculation)
• Extract Readings ( see section Extract Readings)

Gap4 Edit menu

The Edit menu contains options that alter the contents of the database.

• Edit Contig ( see section Editor introduction)
• Join Contigs ( see section Editor joining)
• Save Contig Order ( see section Order Contigs)
• Break Contig ( see section Break Contig)
• Complement a Contig ( see section Complement a Contig)
• Order Contigs ( see section Order Contigs)
• Quality Clip ( see section Quality Clipping)
• Difference Clip ( see section Difference Clipping)
• Double Strand ( see section Double Strand)
• Disassemble Readings ( see section Break Contig)
• Enter Tags ( see section Enter Tags)
• Edit Notebooks ( see section Notes)
• Doctor Database ( see section Doctor database)

Gap4 View menu

The View menu contains options to look at the data at several levels of detail, and analytic functions which present their results graphically.

• Contig Selector ( see section Contig Selector)
• ResultsManager ( see section Results Manager)
• Find Internal Joins ( see section Find Internal Joins)
• Find Read Pairs ( see section Find Read Pairs)
• Find Repeats ( see section Find repeats)
• Check Assembly ( see section Check Assembly)
• Sequence Search ( see section Find Oligos)
• Template Display ( see section Template Display)
• Show Relationships ( see section Show Relationships)
• Restriction Enzyme map (see section Restriction Enzyme Search)
• Stop Codon Map ( see section Stop Codon Map)
• Quality Plot ( see section Quality Plot)
• List Confidence ( see section List Confidence)
• Reading Coverage Histogram ( see section Reading Coverage Histogram)
• Read-Pair Coverage Histogram ( see section Read-Pair Coverage Histogram)
• Strand Coverage ( see section Strand Coverage)
• Confidence Values Graph ( see section Confidence Values Graph)

Gap4 Options menu

The Options menu contains options for configuring gap4.

• Consensus Algorithm (see section Consensus Algorithm)
• Set Maxseq (see section Set Maxseq)
• Set Fonts (see section Set Fonts)
• Colours (see section The Colour Configuration Window)
• Configure Menus (see section Configuring Menus)
• Set Genetic Code (see section Set Genetic Code)
• Alignment Scores (see section Alignment Scores)
• Trace File Location (see section Trace File Location)

Gap4 Experiments menu

The Experiments menu contains options to analyse the contigs and to suggest experimental solutions to problems.

• Suggest Long Readings ( see section Suggest Long Readings)
• Suggest Primers ( see section Suggest Primers)
• Compressions and Stops (see section Compressions and Stops)
• Suggest Probes (see section Suggest Probes)

Gap4 Lists menu

The Lists menu contains a set of options for creating and editing lists for use in various parts of the program.

• Creation and Editing (see section Lists Introduction)
• Contigs To Readings (see section Contigs To Readings Command)
• Minimal Coverage (see section Lists Minimum Coverage)
• Unattached Readings (see section Lists Unattached Readings)

Gap4 Assembly menu

The Assembly menu contains various assembly and data entry methods.

• Normal Shotgun Assembly (see section Normal Shotgun Assembly)
• Directed Assembly ( see section Directed Assembly)
• Screen Only ( see section Assembly Screen Only)
• Assembly Independently (see section Assembly Independently)
• Cap2 Assembly ( see section Assembly CAP2)
• Cap3 Assembly ( see section Assembly CAP3)
• FAKII Assembly ( see section Assembly FAKII)
• Phrap Assembly ( see section Phrap Assembly)