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.
SEE ALSO¶
/usr/share/doc/ncbi-epcr/README.txt
bioperl(1), re-pcr(1)
AUTHORS¶
This manual page was written by Steffen Moeller <moeller@debian.org> and
Andreas Tille <tille@debian.org> for the
Debian system (but may
be used by others). Permission is granted to copy, distribute and/or modify
this document under the terms of the GNU General Public License, Version 2 any
later version published by the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be
found in /usr/share/common-licenses/GPL.
