Overview
If you have not read through the FPC tutorial and Contig display tutorial,
you should do so, as that will answer many of your questions.
They are both available from www.agcol.arizona.edu.
To see the Main Menu Help, select the Help with the right mouse and pull-down.
All windows use the same conventions. They are:
Click once on a box or any bold string, it will highlight the box/string.
Click a second time and it will bring up a window associated with the
box/string. For example, next to the word 'Project' is the name of
the project. Click it once to highlight it, click
it again and the project window is displayed. Note that the timing of
the double click does not matter, i.e. the second click can be at any
time after the box or text is highlighted. The one exception to this
rule is on the BSS windows, where a fast double-click is required
to view results.
On any window, click in white space (i.e. anywhere there is not
a button or text) with the right mouse button, and a pull-down of
options will appear; continue to hold the mouse button down and
drag the cursor over the desired option.
NOTE: Most windows have a 'close' button. And for all windows, on the
pull-down in white space, there is a 'close'. Use one of these to close
a window (do NOT use the Unix-supplied close on upper left of the window).
A button with a '...' indicates you use the right mouse button
to see a set of functions. In some cases, you can click with the left button
for the default option or a window of options (e.g. select Help
with the right button and a pull-down appears. Select it with
the left button, and this help appears.)
FPC definitions
Buried clones
Buried clones: Say clone 1 has N bands and clone 2 has M bands (N less than
or equal to M), and
all N bands of clone 1 are exactly the same as N of the M bands of clone 2,
then clone 1 can be 'buried' in clone 2.
Clone 1 is often referred to as the child, and clone 2 is referred
to as the parent. This is an 'exact' bury. If a user-defined percentage (default 0.1)
do not match, the clone will be buried as 'approximate'.
Clones are buried automatically by the assembly routines (Main Analysis -- Build
Contigs and Incremental Build, Contig Analysis -- Compute CBmaps). This can
also be done by the user from the Contig Analysis -- Semi-auto edits.
The automatic routines sometimes bury clones as 'pseudo'; this is when the
child does not qualify as an exact or approximate. See the documentation on these
routines to understand the situations in which this happens.
Buried clones are not displayed on the contig display unless requested. All
children and parents have suffixes:
A '*' after a clone name indicates it is a parent clone.
A '=' after a clone name indicates it is an exact match to its parent clone.
A '~' after a clone name indicates it is an approximate match to its parent clone.
A '+' after a clone name indicates it is a pseudo parent clone.
A '#' after a clone name indicates it is a pseudo match to its parent clone.
CB Units
The metric in FPC is the CB unit. The assembly algorithm builds an approximate
restriction map, which it calls a consensus band (CB) map.
The clones are aligned to it for their position. This is also approximate alignment;
note that since there is error and uncertainty in the data, a perfect alignment
is never possible. The length of the clone in the Contig display is equal to the
number of its bands. The length of the contig is equal to the approximate number
of consensus bands.
Q clones
When aligning the bands of a given clone to the CBmap, FPC keeps track of the number of
bands that do not align, and the number of gaps in the alignment. If approximately
50% of the bands do not align, it is called a Q (questionable) clone. If there are
many Q clones in a contig, this often indicates that there is a false positive join.
Anchors (frameworks & placements)
A framework file has markers that have been located on a chromosome
or linkage group. Each marker has a chr/lg assignment, and a
global position that is relative to the start of the chr/lg.
Frameworks are also often called anchors. They are generally
from a genetic map or radiation hybrid map.
A framework can have type F or P, where the F stands for
framework and is well ordered. The P stands for placement, and
is not well-ordered but is known to be located between the two
flanking frameworks. Note the ambiguity -- the set is often referred
to as the framework markers even though it consists of both
frameworks and placements. The set is also referred to as anchors.
For the markers to be shown in FPC,
they need to be located on at least one clone in FPC.
As of V7, the anchors have both a chromosome (or linkage group) assignment
and an anchor position relative to the chromosome.