Query Features BMT

    There are multiple query sequence formats in the Biomolecule Toolkit to filter both natural and unnatural sequences.

    Natural analogue sequences are entered by 1-letter codes, unnatural sequences are entered by multi-letter codes using dot separators between the building blocks.

    Example for natural sequence query: SEQUENCE

    Example for unnatural sequence query: S.dE.Q.U.dE.N.C.dE

    Note: the searches in Biomolecule Toolkit are case-insensitive (e.g. dS is equal to ds)

    Available wildcards

    ‘N’ for nucleic acid sequences

    ‘X’ for amino acid sequences

    ‘*’ for 1, 2… n residues in nucleic acid or amino acid sequences

    Note: oligonucleotide backbone modifications cannot be queried currently.

    Table 1. Single residue wildcards (amino acid sequences)

    Query sequence Target sequence
    HCAYKAMGNMAMCAQRTPY (wild type) HCAYAAMGNMAMCAQRTPY (mutation) HCAYKAMGNMAMCAQRTPYK (insertion) HCAYKAMGNMAMCAQRTPY (deletion)
    HCAYXAMGNMAMCAQRTPY images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/no.png images/download/attachments/20417888/no.png

    Table 2. Multi-residue wildcards (amino acid sequences)

    Query sequence Target sequence
    HCAYKAMGNMAMCAQRTPY (wild type) HCA K KAMGNMAMCAQRTPY (mutation) HCAYKAMGN K MAMCAQRTPY (insertion) HCAYKAMGNMA MCAQRTPY (deletion) HCAYK AYK AMGNMAMCAQRTPY (duplication)
    HCAY*QRTPY images/download/attachments/20417888/yes.png images/download/attachments/20417888/no.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png
    HCAYMGNMQRTPY images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/no.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png
    HCAYMAQRTPY images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/no.png images/download/attachments/20417888/yes.png
    HCAXKAM*QRTPY images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/yes.png images/download/attachments/20417888/no.png