Description
Protein Sequence Homology Search (Using Score Matrix)

Method :

References :

Needleman, S. B. and Wunsch, C. D. :
"A general method applicable to the search for similarities in the amino acid sequences of two proteins",
J. Mol. Biol., vol.48, pp.443-453 (1970).

How to use :

  1. See 'Service status' and confirm the service is ON.
  2. Select 'Database'.
    PDB-REPRDB is available.
  3. Select 'Score Matrix'.
    'BLOSUM45','BLOSUM62','BLOSUM80','PAM120' and 'PAM250' are available.
  4. Set 'Gap Cost'.
    Select 'System default' or 'User defined'
    ( Click System default to see the gap cost table of system default.)
    When you select 'User defined', fill in the 'Gap' penalties.
    • Opening Gap : Cost penalty for opening gap
    • Extension Gap : Cost penalty for extension gap
    Each 'Gap' penalty must be integer and "0 <= Gap_penalty <= 100".
  5. Set 'Search Threshold'.
    Select 'Sorted by Homology Score' or 'Sorted by exact match rate'.
    • Homology Score : that by alignment result with no query gap
    • exact match rate : percentage of identical residues between the two sequences
    Put appropriate values in upper and lower threshold fields.
    ( You can omit both thresholds at a time. The upper and lower thresholds for Homology Score may be automatically filled in, which are suitable for using BLOSUM62.)
  6. Set 'Max. Output Number'.
    The output will be truncated by this number.
  7. Enter any label for your query into 'Query label=' field.
  8. Enter your amino acid sequence into the field 'Input Query Sequence'.
    Two formats are acceptable.
    8.1
    Simple amino acid sequence is acceptable.
    Example : 
    KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLK

    8.2
    Fasta format is acceptable.
    Example : 
    >CSRC_HUMAN
KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLK
    ( If the field 'Query label=' is blank, the label after '>' in the first line will be used as the label for the sequence. The character '>' in the sequence will terminate the sequence, and other non-alphabetical characters will be removed. )

    Minimum length is 20 a.a.

  9. Push 'Service status' button to confirm the service status for your query.
  10. Push 'Reset this form' only if you want to reset the input form.
  11. Then, push 'Submit' button to submit your query to the server.
  12. Results Example