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  • Getting the protein Domain architecture from a domtblout

    Hello Everyone

    I have a million protein sequences that I ran against Pfam and now I have the corresponding domtblout files. I would like to get the summary architectures for each of these proteins. Someone has written a script in Bioperl on biostar.org, but I cannot get it to work. Is there a non-bioperl method of extracting these architectures from domtblout. I can use evalue or coverage as cut-off to resolve the domain overlaps.

    Thanks
    Abhijit

  • #2
    Originally posted by gen2prot View Post
    Someone has written a script in Bioperl on biostar.org, but I cannot get it to work.
    We will need some more information to help. What script are you referring to? Also, there is no way to determine what "cannot get it to work" means. There are numerous ways to summarize domain matches and depending on what you want, it should be easy to calculate the matches for each sequence. It sounds like someone already has a solution for your question, so the best place to start would be looking at existing scripts/methods.

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