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.