BLASTScope Option Help
  • -s <sort order by ...> (Integer {1-7})
    Specification of the element which sorts.
      1 = bitScore (default)
      2 = query from
      3 = definition
      4 = alignment length

    When "-s 2" is specified and two or more HSP(The continuous homology high domain) are in one HIT(homology was accepted arrangement of DB for BLAST) it sorts by HSP which was the highest as for the score.


  • -h <HSP view mode> (Integer {0,1})
    Specification in HSP (high-scoreing segment pair) display mode.
      0 = All Affair (default)
      1 = 1 Affair

    If specification of "-h 1", only one HSP is displayed about one HIP. HSP is displayed what has highest bit-score.


  • -w <image width> (Integer) default = 1000
    Specification of picture width

    The width of a picture can be specified. (Unit:pixel)


  • -a <StartBP EndBP> (Integer)
    The display domain of Query is specified.

    It can be displayed that only the arrangement of the database which has homology in a part of domain and its domain among Query (inquiry) arrangement.
    ---------------------------------------------------------------------
    Example) $ blastScope -i test.xml -a 3000 10000
    ---------------------------------------------------------------------


  • -m <DrawMode> (Integer {0,1})
    Specification in the drawing mode.
      0 = Usually Mode
      1 = Group Mode

    When "-m 1" (group mode) is specified, all homologous domains are collectively expressed to a party as the usual data.
    And, when the file which became the origin of the database for BLAST(notes line of the file of multi-FASTA form. The line which starts in ">".) is the character sequence which starts in ">group:(number) |", in this number, a group division is performed and it displays on one sequence collectively for every group.


  • -c <Marker Color> (default : use several colors)
    Specification of a marker color.

    format: " -c (red),(green),(blue)"
    The color of a marker displayed in numerical of each color:0 - 255 picture can be specified.
    When not specifying this "-c" option (default), it is displayed in two or more colors.
    In two or more color display, a marker is displayed and a display color is changed by the rate (identity/alinment length) of coincidence of the arrangement for reference and query arrangement.

    when this option is specified, a marker is displayed and coincidence of arrangement is comparatively alike and the depth of a display color is made to correspond by one color.

    ---------------------------------------------------------------------
    ) $ blastScope -i test.xml -c 100,255,150
    ---------------------------------------------------------------------


  • -r <Draw Marker Rim> {T,F} (default = T)
    Existence of a frame display of a marker.

    It can specify whether the frame of a marker is displayed.
    When T (default) is specified, it is black (in full coincidence, a red frame is displayed.). Specification of F does not display a frame.