CDR are not being recognized

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    • May 23, 2016 at 10:03 pm #2428
      Anonymous

        Hi!!

        I had been suscesfully using ROSIE to generate Fab models for a while and lately the server has not able to recognize the CDRL3 and CDRH3 in my antibody sequences. I also tried a sequence that was previously used and modeled but now the server gave an error   


        
ERROR: CDR L3 cannot be recognized !!!  L3 pattern: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y)

        and I dont undestand why  the CDR cant not be recognized now. The pattern of the input seqeunces looks correct. 

        I would really aprreacite some help in this matter

        Thanks

      • May 24, 2016 at 1:46 pm #11594
        Anonymous

          Thanks for bringing this to our attention, wildchipiron.  In the last month, we added multi-template grafting to the server, and perhaps the regular expressions changed inadvertently.  We will check it out.

        • May 25, 2016 at 9:54 pm #11596
          Anonymous

            wildchipiron,

            I looked at the input to a failed run from ROSIE user chipiron (I’m assuming that’s you); the input query_h and query_l have whitespace in the FASTA sequence line, which the regular expressions are trying to read as amino acids. If you remove the whitespace to leave a single FASTA line, the sequence should run properly.

            Best,

            Nick

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