e-pcr(1) [debian man page]
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: -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. February 2004 E-PCR(1)
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RE-PCR(1) General Commands Manual RE-PCR(1) NAME
re-PCR -- Find sequence tagged sites (STS) in DNA sequences SYNOPSIS
re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...] re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...] re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]] re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...] DESCRIPTION
Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by per- forming STS and primer searches. OPTIONS
-p=hash-file Perform primer lookup using hash-file -P=hash-file Perform primer lookup using hash-file -s=hash-file Perform STS lookup using hash-file -S=hash-file Perform STS lookup using hash-file -n=mism Set max allowed mismatches per primer for lookup -g=gaps Set max allowed indels per primer for lookup -m=margin Set variability for STS size for lookup -l Use presize alignments (only if gaps>0) -G Print alignments in comments -d=min-max Set default STS size -r=+|- Enable/disable reverse STS lookup -O=+|- Enable/disable syscall optimisation -C=batchcnt Set number of STSes per batch -o=outfile Set output file name -q Quiet (no progress indicator) EXAMPLE
famap -tN -b genome.famap org/chr_*.fa fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200 See famap(1) and fahash(1) SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt bioperl(1), e-pcr(1), famap(1) and fahash(1) AUTHORS
This manual page was written by 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. April 2008 RE-PCR(1)