• Scanning sequence similarity
  • DNAMAN scans all the sequence records in the default database to search for homology sequences of the current sequence. If the default database contains DNA sequences, the default sequence has to be DNA sequence. If the default database contains protein sequences, the default sequence has to be protein sequence. DNAMAN will use fast alignment method to scan the database for sequence similarity. You have the choice of using fast alignment or optimal alignment for final output of the result.

    Choose the Database | Scan for Sequence Similarity command to open a Pairwise Alignment dialog box. The scanning is performed with pairwise alignment. After scanning, qualified records will be aligned to the query sequence. The Cutoff score is used to qualify a record as homology sequence. There are two scores of cutoff: one is used during database scanning and the other is used in final alignment. If a record fails any of the two qualifications, it will not be selected.

    You can the parameters for alignment; K-tuple and Gap penalty for fast alignment (see the section IX.2), Gap open and Gap extension for optimal alignment (see the section IX.2). If you scan for protein sequences, you can select different weight matrices, and have the option to show similar amino acids in the alignment.

    The retrieved sequence information is shown in a text window. The homology of two sequences is calculated using the formula described in the section IX.2.