AGCoL TCW Documentation UA
TCW Home | Download | Docs | Tour
bullet Getting started
  Summary A summary of the input, processing and suite of programs.
  TCW Tour Snapshots of different TCW screens.
  InstallationInstalling TCW and other necessary and optional software.
bullet 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
bullet Processing Details
  Annotate Details Removing, adding, updating annotation; pruning hits
  ORF finder Description of options, algorithm, outputs, and results.
  Assembly Details Not typically necessary2
bullet Other documentation
  ExternalExternal packages used by TCW
  MacOS Installing MySQL, etc on MacOS
  Trouble Shooting Potential technical difficulties.
   Release NotesRelease detail since v1.0
  HelpAll TCW programs have Help pop-ups on every display.
  Main Page TCW home page
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. The TCW assembly does not work for high-throughput sequencing reads, but is still occasionally useful for Sanger ESTs or assembling multiple sets of transcripts.
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