T-ACE Manual

Why T-ACE

Installation

• Setting up a T-ACE database server

• Setting up a T-ACE client

• Different T-ACE versions

• Required software

T-ACE Manager

T-ACE

Introduction

• Configure the T-ACE

• Sequence types

Menus

• Config menu

  • Change user password
  • Database browser
  • Database connection
  • Database info
  • Blast parameters
  • Blast results
  • InterProScan results
  • Primer3
  • Refresh configuration
  • Repeats
  • Save configuration
  • Set BrowserPath
  • Set HomeFolder
  • Set ProteinTranslationTable
  • Tabs

• Edit menu

  • Add sequences
  • Edit DB
    • Add ACE file
    • Add blast results
    • Add InterProScam results
    • Add nucleotide file
    • Add protein file
    • Add SAM file
    • Change comment
    • Create database copy
    • Delete selected contigs
    • Delete selected hits
    • New nucleotide sequence
    • Update
      • Update blast2interpro entries
      • Update coverage
      • Update database info
      • Update descriptions
      • Update domain2interpro entries
      • Update GO-Statistic
      • Update KEGG-Maps
      • Update read distribution
      • Update read status
      • Update sequence entries
  • Invert selection
  • Remove selected sequences
  • Save
  • Show

• File menu

  • Delete selected DB
  • Export
  • Import
  • Load config
  • Log in
  • New DB
  • New project
    
  • Open project
    
  • Quit
    
  • Save config
    
  • Save project
    
  • Select DB
    

• Help menu

• Modules menu

  • Blast align
  • Create Blast-Database
  • NCBI-Blast
  • Run compare

• Tabs menu

• Tools menu

  • Expression analysis
  • InterProScan
    
  • Phobos
  • Primer3
  • Search

Tabs

• Blast

• Blast results

• Comment
  

• Database browser
  

• Database info
  

  • Add run
  • Coverage
  • 'Export'-buttons

• Database statistics
  

  • Coverage
  • Expression analysis
  • Frequency

• Domain viewer
  

• GO hits
  

• GO statistics
  

• InterProScan results
  

• KEGG
  

• KEGG maps
  

• Mapping
  

• Primer
  

• Process
  

• Protein viewer
  

• Repeats
  

• Sequence browser
  

• Sequence viewer
  

Windows

• Coverage

• Edit sequence

  • Contig sequence
  • Open reading frames
  • Selected sequence
  • Right-click menu
    • Add to blast
    • Coverage
    • Delete
    • Insert
    • New sequence
    • Refresh
    • Replace with
    • Search
    • Show complementary strand
    • Translate whole frame

• New sequence

• Project tabs

• Right-click menus

  • Add to blast
    

  • Copy cell
    

  • Copy column
    

  • Copy row
    

  • Copy table
    

  • Coverage
    

  • Create primer
    

  • Edit sequence
    

  • Export reads
    

  • Hide/Show column
    

  • New sequence
    

  • Save config
    

  • Search
    

  • Search repeats
    

  • Show all hits
    

  Creating the first database

  Writing modules