e-PCR1
Find sequence tagged sites (sts) in dna sequences
Usage
e-PCR [-hV]
[posix-options]
stsfile
[fasta ...]
[compat-options]
Overview
The program substitutes blast in the location of pairs primers on the genome that may yield a PCR product.
Options
posix-options are:
-
-m=## -
Margin (default 50)
-
-w=## -
Wordsize (default 7)
-
-n=## -
Max mismatches allowed (default 0)
-
-g=## -
Max indels allowed (default 0)
-
-f=## -
Use ## disontiguous words, slow if ##>1
-
-o=## -
Set output file
-
-t=## -
Set output format:
|
1 - classic, range (pos1..pos2) |
|
|
2 - classic, midpoint |
|
|
3 - tabular |
|
|
4 - tabular with alignment in comments (slow) |
-
-d=##-## -
Set default size range (default 100-350)
-
-p=+- -
Turn hits postprocess on/off
-
-v=## -
Verbosity flags
-
-a=a|f -
Use presize alignments (only if gaps>0), slow
-
a - Always or f - as Fallback
-
-x=+- -
Use 5'-end lowercase masking of primers (default -)
-
-u=+- -
Uppercase all primers (default -)
compat-options (duplicate posix-options) are
M=##
|
Margin (default 50) |
|---|---|
W=##
|
Wordsize (default 7) |
N=##
|
Number of mismatches allowed (default 0) |
G=##
|
Max indels allowed (default 0) |
F=##
|
Use ## discontinuous words |
O=##
|
Set output file to ## |
T=##
|
Set output format (1..3) |
D=##-##
|
Set default size range |
P=+-
|
Postprocess hits on/off |
V=##
|
Verbosity flags |
A=a|f
|
Use presize alignments (only if gaps>0), slow |
|
a - Always or f - as Fallback |
|
X=+-
|
Use 5'-end lowercase masking of primers (default -) |
U=+-
|
Uppercase all primers (default -) |
-
-mid -
Same as T=2
For information about further options just call e-PCR without any options.
Releases
11 releases since Debian 3.1 (Sarge); the text changed 2 times.
-a since Debian 5.0 (Lenny);
-d since Debian 5.0 (Lenny);
-f since Debian 5.0 (Lenny);
-g since Debian 5.0 (Lenny);
-m since Debian 5.0 (Lenny);
-n since Debian 5.0 (Lenny);
-o since Debian 5.0 (Lenny);
-p since Debian 5.0 (Lenny);
-t since Debian 5.0 (Lenny);
-u since Debian 5.0 (Lenny);
-v since Debian 5.0 (Lenny);
-w since Debian 5.0 (Lenny);
-x since Debian 5.0 (Lenny).