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E-PCR(1) General Commands Manual E-PCR(1)

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:

Margin (default 50)
Wordsize (default 7)
Max mismatches allowed (default 0)
Max indels allowed (default 0)
Use ## disontiguous words, slow if ##>1
Set output file
Set output format:
1 - classic, range (pos1..pos2)
2 - classic, midpoint
3 - tabular
4 - tabular with alignment in comments (slow)
Set default size range (default 100-350)
Turn hits postprocess on/off
Verbosity flags
Use presize alignments (only if gaps>0), slow
a - Always or f - as Fallback
Use 5'-end lowercase masking of primers (default -)
Uppercase all primers (default -)

compat-options (duplicate posix-options) are

Margin (default 50)
Wordsize (default 7)
Number of mismatches allowed (default 0)
Max indels allowed (default 0)
Use ## discontinuous words
Set output file to ##
Set output format (1..3)
Set default size range
Postprocess hits on/off
Verbosity flags
Use presize alignments (only if gaps>0), slow
a - Always or f - as Fallback
Use 5'-end lowercase masking of primers (default -)
Uppercase all primers (default -)
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.

February 2004