Integral membrane proteins encoded by plant viruses have roles in cell-to-cell movement, targeting of replication proteins of RNA viruses to the endoplasmic reticulum and in transmission by some vectors (Adams & Antoniw in press). We have developed the TMpredict software to use the database and provide an easy method for preliminary assessment of the likely presence of transmembrane regions in virus open reading frames. This uses the established TMpred method (Hofmann and Stoffel, 1993. TMbase - a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374:166).
TMpredict is a web-enabled Windows client application that uses the DPVweb database. One or more sequences of any of the viruses contained can easily be selected and one or more of the ORFs are translated into their amino acid sequences. The TMpred method is then applied and a summary of the number of TM domains identified is provided. Further information can be obtained for each ORF giving the detailed TMpred scores and a graphical output. The program greatly simplifies the work needed for analysis and we have already used the software to survey the occurrence of transmembrane regions in each completely sequenced gene of all plant viruses. The program is available free and, provided that you have an active internet connection, it will run on your PC, using the DPVweb database at this web site.
The software is available as a zip file:
The program is largely intuitive but you can obtain full instructions here .