Whith Chromium derivated browsers the alignment is slightly shifted, unfortunately this cannot be patched on our side

How To
  • Query section (1) Pasting the sequencing
    • Copy the sequences (in fasta format) in the "Query" section.
    • The fasta format is absolutely mandatory
    • Some controls are done for usual corrections, but the software do not manage odds.
    • You can give a name to your batch.
    • TB-DB
  • Query section (2) Choosing the sequence database
    • You must choose the database corresponding to the gene that you have sequenced from the menu
  • Running MUBII
    • Click the [Run now and wait] button
    • You get the result in a new page
  • Running the verification step
    • Click the [Run now and wait] button
    • Do not enter anything nor choosing a database
    • Click the [Run the PPF now and wait] button on this control page
  • Interpreting MUBII results
    • Nucleic point of view
      • The result appears in a new html page embedding the presentation of the DNA and protein alignments, along with the sequence of the wild-type strain.
      • The first section of the result pages concerns the nucleotide sequence. This section shows the DNA alignment of the query against the wild-type sequence and highlights mutations.
      • TB-DB
      • When mutations are detected, alerts are printed to point out the position and the type of the mutation, its status (already described or unknown, therapeutic relevance), and situations like frameshift.
      • At the end of this section, the name of the best matching sequence in the BLAST of the query against the reconstructed database of mutated sequences is shown. Access to the whole BLAST results is also possible.
      • Because only a few strains of M. tuberculosis carry double mutations, the database contains only singly-mutated sequences.

    • Proteic point of view
      • The second section concerns the protein corresponding to the nucleic core sequence.
      • TB-DB
      • This section shows the peptide-level alignment of the query against the wild-type sequence and the position of mutations.
      • The alignment is deduced from the nucleic alignment and highlights the mutations and the observed changes in case of frameshift.
      • In this last case, as the gaps are not introduced, the picture shows the actual changes observed in the query.
      • When a stop-codon mutation is created a specific alert is highlighted and the protein is shown in its shortened version.