Description
Protein Sequence Homology Search (Using exact match rate)

Method :

Needleman-Wunsch style dynamic-programming method.
Query sequence is compared to all sequences in the specified database (SWISS-PROT protein sequence database, or PDB-REPRDB structure database). The best pairwise alignment between the query and a candidate sequence is calculated by rigorous dynamic-programming method. In order to reduce output, ID% (percentage of identical amino-acid residues between corresponding residue pairs in the two compared sequences) threshold can be specified.

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 and SWISS-PROT are available.
  3. Set 'Search Threshold'.
    'Sorted by exact match rate' is available.
    • 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. )
  4. Set 'Max. Output Number'.
    The output will be truncated by this number.
  5. Enter any label for your query into 'Query label=' field.
  6. Enter your amino acid sequence into the field 'Input Query Sequence'.
    Two formats are acceptable.
    6.1
    Simple amino acid sequence is acceptable.
    Example : 
    KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLK

    6.2
    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. )

    Maximum length is 2,000 a.a.
    If you selected Database:SWISS-PROT, sequence length =< 300 a.a.

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