Getting started |
| | Summary
| A summary of the input, processing and suite of programs.
|
| | TCW Tour |
Snapshots of different TCW screens. |
| | Installation | Installing 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
|
|
| Processing Details |
| | Annotate Details |
Removing, adding, updating annotation; pruning hits |
| | ORF finder |
Description of options, algorithm, outputs, and results. |
| | Assembly Details |
Not typically necessary2 |
|
| Other documentation |
| | External | External packages used by TCW |
| | 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.
|
| | 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. |
