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Searching for TCW
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Starting with release v2.3, runSingleTCW and runMultiTCW can use blast+, usearch or diamond for annotation.

Using different search programs in TCW

  1. Download (blast is required, the other two are optional):
     
  2. Put the search path in the HOSTS.cfg file (see HOSTS.cfg for more detail):
    blast_path =
    diamond_path =
    usearch_path =
    
It is highly recommended to use Diamond as it is SO much faster than Blast+. The TCW default parameters have been set so that Diamond gets as good or better results than Blast+ when annotating transcripts with protein sequences; see Results.

 

 

 

 

  Execute runSingleTCW

When you add an annoDB (i.e. database to search against such as UniProt), you have the option of selecting the search program to use. It will only list the programs specified in the HOSTs.cfg file.

 

 

 

 

 

 

Execute runMultiTCW

Similar to runSingleTCW for AA self-blast. The search program and parameters can be set using the "Setting" menu.

runSingleTCW AnnoDB table interface

runSingleTCW AnnoDB add/edit interface

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