The University of Arizona
TCW Documentation Index
AGCoL | TCW Home | Doc Index | singleTCW Guide | DE Guide | multiTCW Guide | Tour
Getting started
  Summary A summary of the input, processing and suite of programs.
  InstallationInstalling TCW and other necessary and optional software.
  
Major documents with step-by-step details using the Demo dataset
  runAS Annotation Setup1 - Getting UniProt, GO, nr, etc for use with runSingleTCW
  runSingleTCW Single species - Building a single species annotated TCW database
  runDE Differential Expression - Add DE to the singleTCW database
  runMultiTCW Multiple species - Building a comparison database from single TCW databases
  viewSingleTCW and viewMultiTCW Viewing results - the user manual is built into the programs Help pages; also see Single Tour and Multi Tour.
  
Details
  Updating annotation Removing, adding, updating annotation
  ORF finder Description of options, algorithm, outputs, and results.
  Assembly Details Not typically necessary2
  
Other docs
  External SoftwarePackages used by TCW
  TCW Tour Snapshots of different TCW screens
  Mac-OSX Installing MySQL, etc on Mac-OSX
  Trouble Shooting Potential technical difficulties.
   Release NotesRelease detail since v1.0
  HelpAll TCW programs have Help pop-ups on every display.
1The sequences that are loaded into TCW (e.g. transcripts, proteins) are searched against one or more databases for annotation; these annotation databases are referred to as "AnnoDBs". When UniProt is used for annotation, TCW provides GO, KEGG, EC, Interpro and Pfam annotations.
2TCW can be used with already assembled transcripts, proteins or mRNA (e.g. predicted genes with introns removed), i.e. the assembly is not usually necessary now. Though the TCW assembly does not work for high-throughput sequencing reads, it is still occasionally useful for Sanger ESTs or assembling multiple sets of transcripts.

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