Sequence Search Types

    Subsequence search, full sequence search

    The subsequence search finds sequences that carry a given part of sequence or sequence motifs described in a query sequence. This type of search is relevant in case of filtering by sequence parts responsible for e.g. structural stability or biological activity. The search takes into account only exact matches within the sequences to be filtered.

    The full sequence search filters based on exact, full-length sequence matches. The query sequence matches only if it possesses all the monomer abbreviations present in a whole sequence to be searched.

    Table 1. Subsequence and full sequence searches

    Query sequence Target sequence Hit
    Full sequence Subsequence
    HCAYKAMGNMAMCAQRTPY HCAYKAMGN MAMCAQRTPY (exact match) images/download/attachments/13109929/yes.png images/download/attachments/13109929/yes.png
    RPHCAYKAMGNMAMCAQRTPYGS (submatch) images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    HCAYKAMGNMAMC V QRTPY (mutation) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png
    HCAYKAMGNMAMCAQRT G PY (insertion) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png
    HCAYKAMGNMA MCAQRTPY (deletion) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png
    HCAYKAMGNMAMCAQRTPY PY (duplication) images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png

    Similarity searches

    Distance-based similarity search

    The distance-based similarity search enables to filter sequence variants which differ in neighbouring motifs, monomer composition and length.

    To perform the search, the distance should be set by providing a number. The value means the number of differences between the query sequence and the target sequences.

    Table 2. Distance-based similarity search

    Query sequence Target sequence Hit
    Distance is exactly 1 Distance is exactly 2 Distance is up to 5
    HCAYKAMGNMAMCAQRTPY HCAYKAMGNMAMCAQRTPY (wild type) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    HCAYKAMGNMAMC V QRTPY (mutation) images/download/attachments/13109929/yes.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    HCAYKAMGNMAMCAQRTPY K (insertion) images/download/attachments/13109929/yes.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    HCAYKAMGNMA MCAQRTPY (deletion) images/download/attachments/13109929/yes.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    HCAYKAMGNMAMCAQRTPY PY (duplication) images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png images/download/attachments/13109929/yes.png
    HC W KAMGNMAMC V QRTPY (mutation) images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png images/download/attachments/13109929/yes.png
    HCAY P KAMGNMAMCAQRTPY K (insertion) images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png images/download/attachments/13109929/yes.png
    HCAYKAMGNMAMCAQRTPY QRTPY (duplication) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    HCAYK HCAYK AMGNMAMCAQRTPY (duplication) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png
    M HCAYK YK AMG Q MAMCAQRTP Y (all types of changes) images/download/attachments/13109929/no.png images/download/attachments/13109929/no.png images/download/attachments/13109929/yes.png