• Sequence Handling and Conversion
  • This chapter explains how to handle DNA and protein sequences in DNAMAN.



    1. Loading sequence into channels
    2. You may choose a sequence once and perform many kinds of analyses on it. This sequence must be loaded into a sequence channel. DNAMAN provides 20 sequence channels to keep active sequences in memory. You can simultaneously analyze and compare all sequences in the channels. You may also switch one sequence to another during analysis without going back to disk files.

      A sequence channel contains not only the sequence, but also related information: 1) Sequence name, 2) sequence type (DNA or Protein), 3) Linear or circular DNA, 4) Analysis region and 5) Annotations.

      There are several methods to load sequences into sequence channels. They are shown in the six sub-menus of Sequence | Load Sequence menu.



    3. Analysis definition
    4. You may change the sequence properties using the Analysis Definition function.

      Choosing the Sequence | Current Sequence | Analysis Definition command opens the Analysis Definition dialog box.

      You can define the following properties of a sequence:



    5. Sequence conversion
    6. DNAMAN can display the current sequence and its related sequences such as reverse complement sequence and double stranded sequence. When a single-stranded sequence is shown, DNAMAN also indicates its nucleotide composition and the predicted molecular weights.

      Choosing the Sequence | Display | Sequence and Composition command invokes a dialog box. You may check six options for DNA sequences: 1) Sequence and Composition; 2) reverse sequence; 3) complementary sequence; 4) reverse complementary sequence; 5) double stranded sequence and 6) RNA sequence. If the default sequence is Protein, only the first option is available.

      If annotations have been defined in a sequence, you have options to include or exclude any of these annotations. The required sequence information will be displayed in a text window. With the features of Excluding and Display Only sequence annotations, you may exclude some sequences (e.g. Introns) from the original sequence, or get exclusively some interesting regions (e.g. Exons).



    7. Draw sequence map
    8. You may draw a map of the current sequence using the Sequence | Draw Sequence Map command. If elements have been defined within the sequence, DNAMAN will incorporate them in the map. You may also add or remove the elements by editing the map. Sequence maps are in DMP format. See the section X.4 about how to modify a DMP file.



    9. Plot DNA properties
    10. You may visualize the thermodynamic properties of a DNA molecule using the Sequence | Plot DNA Properties menu. The plot is drawn in a graphic window. See the section V.5 about handling of the plot window.



    11. Blast document
    12. For searching the homology of a sequence, you may access the BLAST E-mail Server by sending a query sequence to the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. The query sequence will be compared with the DNA or protein sequence databases in NCBI using Basic Local Alignment Search Tool (Blast). You may find more information about the BLAST server from the NCBI web site. You may also refer to the publication of Altschul, S.F. et al., 1990. J. Mol. Biol. 215:403.

      DNAMAN allows you to format the default sequence into a Blast document for accessing the BLAST Server. There are five formats:

      1)Blastn compares a nucleotide query sequence against a nucleotide sequence database.

      2)Blastx compares the six-frame conceptual translation products of a nucleotide query sequence against a protein sequence database.

      3)Tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

      4)Blastp compares an amino acid query sequence against a protein sequence database.

      5)Tblastn compares a protein query sequence with a nucleotide sequence database dynamically translated in all six reading frames.

      For example:

      Blastn

      e-mail to: blast@ncbi.nlm.nih.gov
      PROGRAM blastn
      DATALIB nr
      BEGIN
      >Nt sequence of EXAMPLE1
      TTTGACTGCCACTTCCTCGATGAAGGTTTTACTGCCAAG
      
      

      Blastp

      e-mail to: blast@ncbi.nlm.nih.gov
      PROGRAM blastp
      DATALIB nr
      BEGIN
      >Protein sequence
      FDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILK

      The Blast documents are text files. Save a Blast document and send it to the Blast E-mail Server whose address is displayed in the first line. To obtain instructions on using the Blast E-mail Server, send a message to the following address: blast@ncbi.nlm.nih.gov.

      You may use the Sequence | Current Channel | Analysis Definition command to define any region of the default sequence as a query sequence. You may also modify the content of a Blast document by deleting or adding any nucleotide or amino acid sequence.

      The BLAST documents are derived from a template file (blasttem.dat) that is stored in the DNAMAN system folder. You may modify the template if necessary.