AGCoL TCW - Transcriptome Computational Workbench UA
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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.
   TCW_4.tar.gz    Executables, demos, external packages, R scripts
Summary          Inputs, outputs and processing
Docs Documentation pages
runAS Obtain UniProt and GO for input to runSingleTCW
runSingleTCW Build single species annotated database
runDE Add differential expression
viewSingleTCW Query results of a single species database
runMultiTCW Build multi-species comparison database
viewMultiTCW Query results of multi-species database
DIAMOND Integration of DIAMOND for fast annotation.
ORF finder The algorithm uses hit information and on-the-fly training for a 5th-order Markov score.
Differential Expression Users can supply a file of R commands for DE computation, or use built-in computations.
  C. Soderlund (2022) Transcriptome computational workbench (TCW): analysis of single and comparative transcriptomes. BioRxiv
  C. Soderlund, W. Nelson, M. Willer and D. Gang. (2013) TCW: Transcriptome Computational Workbench. PLoS ONE
Single Table of Sequences
Figure 1: viewSingleTCW - result of a query on DE values.
Sequence frame view
Figure 2: Computed ORF using hit coordinates as a guide.
Alignment of two sequences
Figure 3: viewMultiTCW - dynamic programming alignment of a BBH cluster.

All upgrades starting with TCW v1.3 have been developed by CAS without funding.

This project was funded in part by National Science Foundation grant IOS-1044821.

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.

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