Workshop (V): Family Assignments

Important GCG tools and web sites: Please refer to the Related Material (VII)

To examine whether your sequence contains any known domains/motifs. You can use

  1. GCG's profilescan or
  2. The network tools

Now you have assigned a few genes and you are ready to do protein annotations. Please use what you have learned in "GCG automation" (i.e. create a batch submission file) to do the following analysis:

  1. Calculate the theoretical M.W. (peptidesort)
  2. Estimate the pI value (isoelectric )
  3. Predict whether this protein is a membrane protein (pepplot, peptidestructure, plotstructure, moment )
  4. Predict the protein secondary structure (pepplot, peptidestructure, plotstructure)
  5. Predict the signal peptide sequence (spscan )
  6. Predict the important motifs or sites in your protein (motifs )
  7. Predict whether there is any helix-turn-helix motif in your protein (hthscan )
  8. Predict whether there is any coiled-coil in your protein (coilscan )
  9. Predict whether there is amphipathic helix in your protein (moment, helicalwheel)
  10. Please annotate the putative proteins you assigned on POST (column N)
  11. Please transfer your POST file to FTP to