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 v2.4 (2-20-2018) -- 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.

Summary - inputs, outputs and processing
  Index - into documentation pages
TCW package - jars, demos, external packages, R scripts
  TCW source - source code for developers
  TCW update - jars and R-scripts only for TCW updates
viewSingleTCW - query results of a single species database
  runSingleTCW - build single species annotated database
  runDE - add differential expression
  viewMultiTCW - query comparison results
  runMultiTCW - build comparison database
  Java Applets - demos contained in package

Recent Releases:

  1. Fast searching in TCW: Integration of diamond and usearch for fast annotation.
  2. Location information: Location information (e.g. chromosome, start, end) can be entered.
  3. ORF finder: The algorithm uses hit information and on-the-fly training of usage along with Start/Stop codons.
  4. Differential Expression: Users can supply a file of R commands for DE computation, or use built-in computations.
  5. Release Notes: Provides information on other updates.


  1. C. Soderlund, W. Nelson, M. Willer and D. Gang. (2013) TCW: Transcriptome Computational Workbench. PLoS ONE Link
  2. C. Soderlund, E. Johnson, M. Bomhoff, and A. Descour. (2009) PAVE: Program for Assembling and Viewing ESTs. BMC Genomics 10:400. Link
  3. C. Soderlund, W. Nelson and S. Goff (2014) Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression. 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.

Email Comments To: