| Getting started|
| ||Summary ||A summary of the input, processing and suite of programs.
| ||Installation||Installing TCW and other necessary and optional software.
| Major documents with step-by-step details using the Demo dataset|
||Annotation Setup1 - Getting UniProt, GO, nr, etc for use with runSingleTCW|
||Single species - Building a single species annotated TCW database
||Differential Expression - Add DE to the singleTCW database
||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;
Single Tour and
| ||Updating annotation
||Removing, adding, updating annotation|
| ||ORF finder
||Description of options, algorithm, outputs, and results. |
| ||Assembly Details
||Not typically necessary2 |
| Other docs|
| ||External Software||Packages used by TCW|
| ||TCW Tour ||Snapshots of different TCW screens|
| ||MacOS ||Installing MySQL, etc on MacOS|
| ||Trouble Shooting
||Potential technical difficulties.|
Release Notes||Release detail since v1.0|
| ||Help||All 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.