runMultiTCW takes as input two or more singleTCW databases and builds a multiTCW database
of clustered sequences.
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
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.
- OrthoMCL -
runMultiTCW executes the
orthoMCL scripts and then loads the results into the mTCW database.
- 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.
- User Defined - load a file of clusters where the file format is the orthoMCL format.
(Click any image to see larger)
Add for step 1.
- Select sTCW Database lists
the singleTCW databases to choose from.
- There is a choice of inputting a SMAT file created for
The user must supply this, then
runMultiTCW will run
using the selected SMAT file. Alternatively, the user can input the ORFtranslated
file created during
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
- 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.
- 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.
- Li L, Stoeckert CJ, Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.