Instructions for use of TMpredict software

TMpredict has 6 pages that are used to help select the sequences and features for analysis.

• Genera: This page is used to select the virus for analysis.

  1. Click the Get Genera button to retrieve the complete list of genera in the database. Genera are colour coded to help identify those whose members infect plants, fungi etc. (see the About... Genera colour codes... menu).
  2. Select a genus from the left hand column (using the left mouse button) and use the Get Viruses button used to display the members. This will be the complete list of recognised and tentative members of the genus (there will not be sequences associated with all of them).
     
  3. Select the virus of interest (using the left mouse button) and click on the Get Accnos button.
     

• Accnos: This page lists all the available accessions of the virus previously selected with a brief description of each. Select one or more sequences using the buttons or the check boxes and click on the Get Features button.

• Features: This page lists all the features detected in the sequences selected. Choose one or more features using the check boxes and click on the TM Scan button.

• TM Scan: This page provides the summary output. For each ORF, the numbers of TM domains identified in each orientation is displayed together with the gene name, accession number and coordinates of the ORF. Select a line from the output to obtain more detailed information on the following two pages.

• TM Domains: This page gives the full TMpred prediction output in text form, including all identified TM helices, their positions in the ORF and the calculated scores.

• Graph: This page displays the prediction as a graphical output, where peaks >500 are possible TM helices.

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