-
screen shots
o Input
interface
§
First
screen
§
Open
file – histogram file
§
Control
Bar
·
X-axis
: first 3 divided scale
·
Y-axis
: the 4-th scale bar
·
Depth
1- 3 : showing the edges of relation graph
·
Color
: background color – white and black
·
GeneAnnotationSave button : report the overlapped regions
§
Output
control
·
VIEW
tab 
o
blocks
o
frequency
of genome
o
COG
o
gene
o
COG/gene
name
o
Link
other genomes for constructing relation graph
·
LIST
tab
o
List
of edges : to get a path of some graph, click a edge
in the list.
·
STAT tab
o
Average
score
o
simple
statistic result
·
FILTER
tab
o
Block
Filtering
-
Setting cut_off score for making block node
o
Edge
Filtering
-
Setting range of cut_off score to connect nodes
-
Setting range of length of bloc node
-
Best hit : choose the highest score edge of all edges
·
Screen
for filtering out nodes under edge filter
o Finding
site
§
Scanning
an interesting site
§
Zoom
out
§
Zoom
out and showing the connectivity
·
1/4000
ratio
§
Showing
the list of edges of relation graph
·
List
: display the
position and node number. If there is terminal and not block, the node number
is -1.
§
Showing
a path in the list of relation graph
§
Showing
the sequences of blocks
§
Sample
path which has different information
o
It
may find new fact.
o
Reference
block of genome NC_00921 has no information COG and gene, but matched blocks of
the other genomes have gene information which could be find a new fact.
§
Result
of multiple alignment for selected region using Clustal-w.
o Annotation
of new genome
§
If
we have a new genome without any annotation, COMPAM visualizes a rough
annotation.