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Tour: runAS
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runAS - Annotation Setup

runAS downloads UniProt files and formats them for input to sTCW, and download the GO database to build a local GO database for input into sTCW. See Annotation Setup for details.

runAS performs the following:
  1. Downloads one or more UniProt Taxonomic .dat files and creates FASTA files from them.
  2. Downloads the full SwissProt or TrEMBL, creates subset files by removing entries from the taxonomic downloads, and creates a FASTA file of the remaining entries.
  3. Download the GO schema and data, and creates a GO mySQL database with the mapping of UniProt IDs to the GO, KEGG, EC, Pfam and InterPro.
These are used for annotating a TCW database with runSingleTCW.

The highlighted entries in the figure indicate what has been created, i.e. the invertebrate SwissProt and SwissProt subset.

Other databases, such as Genbank nr, can also be used in runSingleTCW for annotation, but the user must download and format them as FASTA files.

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