The University of Arizona
Tour: runMultiTCW
AGCoL | TCW Home | Doc Index | Tour | runSingleTCW | runDE | viewSingleTCW | runMultiTCW | viewMultiTCW
runMultiTCW
Main Window | Additional Windows | References

runMultiTCW takes as input two or more singleTCW databases and builds a multiTCW database of clustered sequences.

Main window

1. Build database. Define the input databases as described below in "Add for step 1", then press Build database which builds a database of combined sequences.

2. Run BLAST. This creates a file of all sequences and perform blast against itself to determine similar sequences. A user supplied blast file can be supplied in Settings.

3. Add new clusters. These are defined as described below in "Add for step 3". The options are:

  1. OrthoMCL - runMultiTCW executes the orthoMCL scripts and then loads the results into the mTCW database.
  2. Transitive - performs a transitive closure on the sequences to cluster all those with the specified cutoff and similarity, and loads the results into the mTCW database.
  3. User Defined - load a file of clusters where the file format is the orthoMCL format.
One or more clusters can be added with each execution of Add New Cluster, and any cluster can be removed with Remove. This example shows that two sets of clusters have been loaded (the italic cluster name means they are in the database), and a new cluster will be added when Add New Cluster is selected.
(Click any image to see larger)

Additional windows

Go to top
Add for step 1.
  1. Select sTCW Database lists the singleTCW databases to choose from.
  2. There is a choice of inputting a SMAT file created for ESTscan. The user must supply this, then runMultiTCW will run ESTscan using the selected SMAT file. Alternatively, the user can input the ORFtranslated file created during runSingleTCW.
Add for step 3.
As shown, the only necessary parameter for orthoMCL is the inflation. On the drop-down at the top, if the user selects Transitive, the window shows two parameters of Overlap cutoff and Similarity

References

Go to top

  1. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol: 138-148.
  2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
  3. Li L, Stoeckert CJ, Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
Email Comments To: tcw@agcol.arizona.edu