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 products.

       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 sequence 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