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ipcress(1)		      PCR simulation tool		    ipcress(1)

NAME
       ipcress - In-silico PCR experiment simulation system

SYNOPSIS
       ipcress [ options ] <primer file> <sequence paths>

DESCRIPTION
       ipcress is the In-silico	PCR Experiment Simulation System.

       This  is	 a  tool for simulation	of PCR experiments.  You supply	a file
       containing primers and a	set of sequences, and it  predicts  PCR	 prod-
       ucts.

       Ipcress	is  similar  to	 the  e-PCR program from the NCBI, but is much
       faster, and does	not suffer  from  problems  identifying	 matches  when
       there are ambiguity symbols near	primer ends.

       If  you	supply	many primers pairs together, ipcress will simulate the
       PCR experiments in parallel, allowing genome wide simulation  of	 large
       numbers	of experiments.	 It uses many libraries	from the exonerate se-
       quence comparison tool.

INPUT FORMAT
       The input for ipcress is	a simple white-space delimited file describing
       one experiment per line.	 Each line contains the	following 5 fields:

	      id		An identifier for this experiment
	      primer_A		Sequence for the first primer
	      primer_B		Sequence for the second	primer
	      min_product_len	Minimum	product	length to report
	      max_product_len	Maximum	product	length to report

       Here is an example line in this format:

       ID0001 CATGCATGCATGC CGATGCANGCATGCT 900	1100

OUTPUT FORMAT
       The  output  format describes one PCR product per-line, and is prefixed
       by "ipcress:", followed by the following	11 fields:

	      sequence_id     The sequence identifier
	      experiment_id   The PCR experiment id
	      product_length  The PCR product length
	      primer_5	      The 5' primer (either A or B)
	      pos_5	      Position of the 5' primer
	      mismatch_5      Number of	mismatches on 5' primer
	      primer_3	      |
	      pos_3	      |	Same fields for	the 3' primer
	      mismatch_3      |
	      description     A	description of the PCR product

       The description field is	one of the following 4 strings:

	      forward	Normal product,	primer A followed by B
	      revcomp	Normal product,	primer B followed by A
	      single_A	Bad product generated by primer_A only
	      single_B	Bad product generated by primer_B only

       There is	also a human-readable output displayed,	is  not	 designed  for
       parsing (see: --pretty below).

GENERAL	OPTIONS
       Most  arguments	have  short  and  long forms.  The long	forms are more
       likely to be stable over	time, and hence	 should	 be  used  in  scripts
       which call ipcress.

       -h | --shorthelp	<boolean>
	      Show help.  This will display a concise summary of the available
	      options, defaults	and values currently set.

       --help <boolean>
	      This shows all the help  options	including  the	defaults,  the
	      value  currently	set, and the environment variable which	may be
	      used to set each parameter.  There  will	be  an	indication  of
	      which options are	mandatory.  Mandatory options have no default,
	      and must have a value supplied for ipcress to run.  If mandatory
	      options  are  used in order, their flags may be skipped from the
	      command line (see	examples below).  Unlike this  man  page,  the
	      information  from	this option will always	be up to date with the
	      latest version of	the program.

       -v | --version <boolean>
	      Display the version number.   Also  displays  other  information
	      such as the build	date and glib version used.

FILE INPUT OPTIONS
       -i | --input  <path>
	      PCR experiment data in the ipcress file format described above.

       -s | --sequence <paths>
	      Specify  the  sequences.	 Multiple files	may be specified here,
	      which reduces the	FSM building overhead, and makes  ipcress  run
	      faster than running the process separately.

IPCRESS	PARAMETERS
       -m | --mismatch	<mismatches>
	      Specify  the  number of mismatches allowed per primer.  Allowing
	      mismatches reduces the speed of the program as  a	 large	primer
	      neighbourhood  must be constructed, and fewer experiments	can be
	      fitted in	memory prior to	each scan of the sequence databases.

       -M | --memory <Mb>
	      Specify the amount of memory the program should use.   The  more
	      memory  made  available ipcress, the faster it will run, as more
	      PCR experiments can be conducted in each scan  of	 the  sequence
	      databases.   This	 does  not include memory used during the scan
	      (for storing partial  results  and  sequences),  so  the	actual
	      amount of	memory used will be slightly higher.

       -p | --pretty <boolean>
	      Display  results	in  a  human-readable format, not designed for
	      parsing.

       -P | --products <boolean>
	      Display PCR products as a	FASTA format sequence.

       -S | --seed <length>
	      Specifiy the seed	length for the wordneighbourhood for the  FSM.
	      If  set  to zero,	the full primer	is used.  Shorter words	reduce
	      the size of the neighbourhood, but increase the  time  taken  by
	      ipcress to filter	false positive matches.

ENVIRONMENT
       Not documented yet.

EXAMPLES
       ipcress test.ipcress sequence.fasta
	      This is the simplest way that ipcress can	be used.
       ipcress dbsts_human.ipcress --sequence ncbi30/*.fasta --mismatch	1
	      Compare  a input file against a set of fasta files, allowing one
	      mismatch in each primer.

VERSION
       This documentation accompanies version 2.2.0 of the exonerate package.

AUTHOR
       Guy St.C. Slater.  <guy@ebi.ac.uk>.  See	the AUTHORS file  accompanying
       the source code for a list of contributors.

AVAILABILITY
       This source code	for the	exonerate package is available under the terms
       of the GNU general public licence.

       Please see the file COPYING which was distrubuted with this package, or
       http://www.gnu.org/licenses/gpl.txt for details.

       This package has	been developed as part of the ensembl project.	Please
       see http://www.ensembl.org/ for more information.

SEE ALSO
       exonerate(1),e-PCR

ipcress				  March	2003			    ipcress(1)

NAME | SYNOPSIS | DESCRIPTION | INPUT FORMAT | OUTPUT FORMAT | GENERAL OPTIONS | FILE INPUT OPTIONS | IPCRESS PARAMETERS | ENVIRONMENT | EXAMPLES | VERSION | AUTHOR | AVAILABILITY | SEE ALSO

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