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re-pcr(1) [debian man page]

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)

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Bio::PrimerDesigner(3pm)				User Contributed Perl Documentation				  Bio::PrimerDesigner(3pm)

NAME
Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr SYNOPSIS
use Bio::PrimerDesigner; my $pd = Bio::PrimerDesigner->new; # # Define the DNA sequence, etc. # my $dna = "CGTGC...TTCGC"; my $seqID = "sequence 1"; # # Define design parameters (native primer3 syntax) # my %params = ( PRIMER_NUM_RETURN => 2, PRIMER_SEQUENCE_ID => $seqID, SEQUENCE => $dna, PRIMER_PRODUCT_SIZE => '500-600' ); # # Or use input aliases # %param = ( num => 2, id => $seqID, seq => $dna, sizerange => '500-600' ); # # Design primers # my $results = $pd->design( %params ) or die $pd->error; # # Make sure the design was successful # if ( !$results->left ) { die "No primers found ", $results->raw_data; } # # Get results (single primer set) # my $left_primer = $results->left; my $right_primer = $results->right; my $left_tm = $results->lefttm; # # Get results (multiple primer sets) # my @left_primers = $results->left(1..3); my @right_primers = $results->right(1..3); my @left_tms = $results->lefttm(1..3); DESCRIPTION
Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported. METHODS
binary_path Gets/sets path to the primer3 binary. design Makes the primer design or e-PCR request. Returns an Bio::PrimerDesigner::Result object. epcr_example Run test e-PCR job. Returns an Bio::PrimerDesigner::Results object. list_aliases Lists aliases for primer3 input/output options list_params Lists input options for primer3 or epcr, depending on the context method Gets/sets method of accessing primer3 or epcr binaries. os_is_unix Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0. primer3_example Runs a sample design job for primers. Returns an Bio::PrimerDesigner::Results object. program Gets/sets which program to use. run Alias to "design." url Gets/sets the URL for accessing the remote binaries. verify Tests local installations of primer3 or e-PCR to ensure that they are working properly. AUTHORS
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>. LICENSE
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. SEE ALSO
Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::epcr. perl v5.10.0 2009-08-04 Bio::PrimerDesigner(3pm)

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