• Searching in database with single sequence
  • You can search for a nucleotide sequence in a DNA database, and an amino acid sequence in a DNA or protein database.

    Nucleotide Sequence

    Choose the Database | Search for Nucleotide Sequence command to open a dialog box. Searching for a DNA sequence is performed on both strands of all sequence records in the DNA default database. The formats for searching are the same as searching in the current sequence (see the section VIII.1).

    The results are shown in a text window.

    Search in Database:
      ACCGGAT
    
    Seq:EXAMPLE3 + strand
    No.    Pos     Sequence
    #1     457     ccttgACCGGATtgtgg
    
    Seq:PUC18    + strand
    No.    Pos     Sequence
    #1     2207    tagttACCGGATaaggc
    
    Seq:PUC18    - strand
    No.    Pos     Sequence
    #1     328     cgcttACCGGATacctg
    
    Seq:PBR322    + strand
    No.    Pos     Sequence
    #1     2679    cgcttACCGGATacctg
    
    Seq:PBR322    - strand
    No.    Pos     Sequence
    #1     1531    tagttACCGGATaaggc

    Amino acid sequence

    Choose the Database | Search for Amino Acid Sequence command to open a dialog box. You may search for an amino acid sequence from all protein sequence records in the default protein database. You may also search for an amino acid sequence from six reading frames of all sequence records in the default DNA database.

    The formats for searching are the same as the searching in the current sequence (see the section VIII.1).

    The result is shown in a text window.

    Examples:

    1) search in DNA database for amino acid sequence

    Search in Database for AA sequence:
      PLMST
    Maximum mismatch: 1
    
    Name:PUC18   
    Strand plus
    Reading frame 3:
    255     CCTCTAGAGTCGACC
             P  L  E  S  T
    1077    CCAATGATGAGCACT
             P  M  M  S  T
    
    Name:PBR322   
    Strand minus
    Reading frame 2:
    401     CCAATGATGAGCACT
             P  M  M  S  T
    

    2) search in protein database for amino acid sequence

    Search in Database for AA sequence:
      PLMS
    Maximum mismatch: 1
    
    Name:record8
    1634    ldkyfPLDSevtii