Table 1. Examples of different Pintail plot
profiles as generated with a sampling window size of 300.
| Profile |
Anomaly |
Comments |
Profile |
A
|
Chimera
|
Here
only the the 3' end of the query sequence closely matches the subject -
a very characteristic chimeric pattern.
In this example the chimeric AY373422
is compared with the Nitrospira X82559.
Breakpoint* is at approximate E. coli
position 740.
|
AY373422
is, in fact, a three fragment chimera, with sequence up to base
position
~340 from a Gammaproteobacterium (see B), sequence at ~340 to
~740 from
an Alphaproteobacterium (see C), and ~740
onwards from a Nitrospira. |
|
|
B
|
Chimera |
Here
only the the 5' end of the query sequence closely matches the subject -
a very characteristic chimeric pattern.
In this example the chimeric AY373422
is compared with the Gammaproteobacterium Z31658.
Breakpoint* is at approximate E. coli
position 340.
|
AY373422
is, in fact, a three fragment chimera, with sequence up to base
position
~340 from a Gammaproteobacterium, sequence at ~340 to ~740 from
an Alphaproteobacterium (see C), and ~740
onwards from a Nitrospira (see
A). |
|
|
C
|
Chimera |
The
dip in the profile is suggestive of a three fragment chimera, with the
middle fragment of the query more closely matching the subject than the
remainder of the query.
In this example the
chimeric AY373422
is compared with the Alphaproteobacterium DQ103607.
Breakpoints* are at approximate E. coli
positions 340 and 740.
|
AY373422
is, in fact, a three fragment chimera, with sequence up to base
position
~340 from a Gammaproteobacterium (see B), sequence at ~340 to
~740 from
an Alphaproteobacterium, and ~740 onwards
from a Nitrospira (see A). |
|
|
D
|
Chimera |
The
dip in the profile is highly suggestive of a three
fragment chimera, with the middle fragment of the query more closely
matching the subject than the remainder of the query.
In this example the chimeric U10877
is compared with the Gammaproteobacterium AY586400.
Breakpoints* are at approximate
E. coli positions 790 to 1130. |
|
E
|
Chimera |
This
profile is highly suggestive of a three
fragment chimera, with the 5' and 3' ends of the query both closely
matching the subject, yet the middle region is very different.
In this example the chimeric U10877
is compared with the Bacteriodetes AY856450. Breakpoints*
are at approximate E. coli positions
790 to 1130.
|
 |
F
|
Poor
sequence assembly
|
This
sharp, angular, profile is typical of a poorly assembled sequence with
a whole stretch of sequence missing from the query.
In this example the poorly constructed Z94005
is compared with AY922120.
Sequence of approximately*
200 bases in length is missing from Z94005; clearly the 5' and 3' ends of this sequence have been
concatenated without any attention given to actual sequence homology.
|
 |
|
|
