homology modeling- Error: length mismatch between sequence and alignment.

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    • #1422


        As I run homology modeling on Rosetta 3.4, I get an error message: “Error: length mismatch between sequence and alignmentproblem with sequence:” I checked my input files and the script of SequenceAlignment.cc that produces the message. My files seem to be fine. I am using general format for alignment file. My question is, what sequences are being compared to produce this message. Thanks.

        Here is an excerpt of script:

        void SequenceAlignment::data_integrity_check() const {
        for ( Size jj = 1; jj <= size(); ++jj ) {
        if ( sequences_[jj]->length() != length() ) {
        std::string msg( “Error: length mismatch between sequence and alignment” );
        msg += “problem with sequence: ” + sequences_[jj]->to_string();
        msg += “alignment: ” + to_string();
        utility_exit_with_message( msg );

      • #7867

          If I’m not mistaken, you’re giving a .fasta file of the sequence that you want to model, and an alignment.filt file containing an alignment of that sequence with each of the homologs you wish to model against.

          What this excerpt is doing is checking that each sequence in the alignment is the same length. I’m not 100% sure of how the alignments are loaded, but I think each pair is loaded as a separate SequenceAlignment, so you only need to make sure that each pair matches in total length, gaps inclusive. (Note that you should also make sure that each reference sequence in your pair, ignoring gaps, matches the input sequence from the .fasta.)

          If you can’t find the length mis-match, I would suggest posting your .fasta and alignment files here. (Note you may need to change the extension to .txt to upload them.)

        • #7874

            Thank you for the reply. I solved the problem by setting ‘unwrap text’ setting in my text editor and writing sequences in one line.

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