e-PCR(1)
e-PCR — Find sequence tagged sites (STS) in DNA sequences
Description
E-PCR
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:
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-m=## |
Margin (default 50) |
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-w=## |
Wordsize (default 7) |
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-n=## |
Max mismatches allowed (default 0) |
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-g=## |
Max indels allowed (default 0) |
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-f=## |
Use ## disontiguous words, slow if ##>1 |
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-o=## |
Set output file |
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-t=## |
Set output format: |
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1 - classic, range (pos1..pos2) |
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2 - classic, midpoint |
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3 - tabular |
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4 - tabular with alignment in comments (slow) |
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-d=##-## |
Set default size range (default 100-350) |
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-p=+- |
Turn hits postprocess on/off |
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-v=## |
Verbosity flags |
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-a=a|f |
Use presize alignments (only if gaps>0), slow |
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a - Always or f - as Fallback |
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-x=+- |
Use 5’-end lowercase masking of primers (default -) |
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-u=+- |
Uppercase all primers (default -) |
compat-options (duplicate posix-options) are
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M=## |
Margin (default 50) |
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W=## |
Wordsize (default 7) |
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N=## |
Number of mismatches allowed (default 0) |
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G=## |
Max indels allowed (default 0) |
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F=## |
Use ## discontinuous words |
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O=## |
Set output file to ## |
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T=## |
Set output format (1..3) |
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D=##-## |
Set default size range |
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P=+- |
Postprocess hits on/off |
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V=## |
Verbosity flags |
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A=a|f |
Use presize alignments (only if gaps>0), slow |
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a - Always or f - as Fallback |
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X=+- |
Use 5’-end lowercase masking of primers (default -) |
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U=+- |
Uppercase all primers (default -) |
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-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.
See Also
- bioperl(1)
- re-pcr(1)