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.
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Example) $ blastScope -i test.xml -a 3000 10000
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- -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.
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—á) $ blastScope -i test.xml -c 100,255,150
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- -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.
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