The University of Arizona
TCW: Transcriptome Computational Workbench
AGCoL | TCW Home | Doc Index | singleTCW Guide | DE Guide | multiTCW Guide | Tour
This project is funded in part by National Science Foundation grant IOS-1044821.
All upgrades starting with TCW v1.3 have been developed by CAS without funding.

TCW v2.9 (21Oct2018) -- see Release Notes. TCW provides analysis and query for sequences (transcriptome, proteome), and comparison of species sequences. TCW uses Java, mySQL, optionally R, and various External packages. It has been tested on Linux and Mac.

Download
 
TCW packagejars, demos, external packages, R scripts
TCW sourcesource code for developers
TCW updatejars and R-scripts only for TCW updates
  
Documentation
 
Summary         inputs, outputs and processing
Indexof documentation pages
  
Tour
 
runASobtain UniProt and GO for input to runSingleTCW
runSingleTCWbuild single species annotated database
runDEadd differential expression
viewSingleTCW query results of a single species database
runMultiTCWbuild multi-species comparison database
viewMultiTCWquery results of multi-species database
  
Demos
  Java demos     demos contained in package
  
Recent Features
 
ORF finder The algorithm uses hit information and on-the-fly training for a 5th-order Markov score.
Fast searching Integration of diamond and usearch for fast annotation.
Locations Location information (e.g. chromosome, start, end) can be entered.
Differential Expression Users can supply a file of R commands for DE computation, or use built-in computations.
  
Reference
 C. Soderlund, W. Nelson, M. Willer and D. Gang. (2013) TCW: Transcriptome Computational Workbench. PLoS ONE Link
  
NSF Disclaimer
  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Figure 1: viewSingleTCW - result of a query on DE values.

Figure 2: Computed ORF using hit coordinates as a guide.

Figure 3: viewMultiTCW - dynamic programming alignment of a BBH cluster.
Email Comments To: tcw@agcol.arizona.edu