This is the command e-PCR that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
e-PCR — Find sequence tagged sites (STS) in DNA sequences
SYNOPSIS
e-PCR [-hV] [posix-options] stsfile [fasta ...] [compat-options]
DESCRIPTION
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.
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