General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Functional domain analysis of protein sequences using InterProScan

There’s a new tool in MacVector 15 that allows you to do functional domain analysis on your protein sequence using the InterProScan service. InterPro contains multiple databases of protein families, domains and motifs and InterProScan will submit a protein sequence to a search of these databases. It will also do extra analysis such as transmembrane region analysis using TMHMM and other tools. For MacVector 15 you can submit your protein sequence to an InterProScan search and also annotate results directly back to your sequence.

  • Open your protein sequence.
  • Run DATABASE | INTERPROSCAN SEARCH
  • When the job has finished click VIEW to see the results.
  • Click any “hotlinks” to see the original database entry for a “hit”.
  • Choose the most appropriate result for the particular hit that you want to annotate back to your protein sequence.
  • Click the small cross at the right side of the hit.
  • Switch to the FEATURES tab of your protein sequence.
  • Find the PROTEIN_MATCH feature that you have just added and double click on it.
  • In the FEATURES EDITOR click on the FEATURES KEYWORD list and choose the most appropriate FEATURE KEYWORD for your new feature. For example for an Unintegrated Signature from TMHelix choose TRANSMEM.
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