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
  Annotation Setup1 runAS - Getting UniProt, GO, nr, etc for use with runSingleTCW
  Single species runSingleTCW - Building a single species annotated TCW database
  Differential Expression runDE - Add DE to the singleTCW database
  Multiple species runMultiTCW - Building a comparison database from single TCW databases
  Viewing results viewSingleTCW and viewMultiTCW - the user manual is built into the programs Help pages; also see Single Tour and Multi Tour.
Annotation details
  Searching for sTCW and mTCW Using the super-fast diamond or ublast in place of blast
  ORF finder Description of options, algorithm, outputs, and results.
  Updating annotation Removing, adding, updating annotation
Other docs
  External SoftwarePackages used by TCW
  TCW Tour Snapshots of different TCW screens
  Assembly Details Not typically necessary2
  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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