1ipcress(1) PCR simulation tool ipcress(1)
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6 ipcress - In-silico PCR experiment simulation system
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9 ipcress [ options ] <primer file> <sequence paths>
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13 ipcress is the In-silico PCR Experiment Simulation System.
14 This is a tool for simulation of PCR experiments. You supply a file
16 containing primers and a set of sequences, and it predicts PCR prod‐
17 ucts.
18 Ipcress is similar to the e-PCR program from the NCBI, but is much
20 faster, and does not suffer from problems identifying matches when
21 there are ambiguity symbols near primer ends.
22 If you supply many primers pairs together, ipcress will simulate the
24 PCR experiments in parallel, allowing genome wide simulation of large
25 numbers of experiments. It uses many libraries from the exonerate
26 sequence comparison tool.
27
29 The input for ipcress is a simple white-space delimited file describing
30 one experiment per line. Each line contains the following 5 fields:
31 id An identifier for this experiment
33 primer_A Sequence for the first primer
34 primer_B Sequence for the second primer
35 min_product_len Minimum product length to report
36 max_product_len Maximum product length to report
37 Here is an example line in this format:
39 ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100
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43 The output format describes one PCR product per-line, and is prefixed
44 by "ipcress:", followed by the following 11 fields:
45 sequence_id The sequence identifier
47 experiment_id The PCR experiment id
48 product_length The PCR product length
49 primer_5 The 5' primer (either A or B)
50 pos_5 Position of the 5' primer
51 mismatch_5 Number of mismatches on 5' primer
52 primer_3 |
53 pos_3 | Same fields for the 3' primer
54 mismatch_3 |
55 description A description of the PCR product
56 The description field is one of the following 4 strings:
58 forward Normal product, primer A followed by B
60 revcomp Normal product, primer B followed by A
61 single_A Bad product generated by primer_A only
62 single_B Bad product generated by primer_B only
63 There is also a human-readable output displayed, is not designed for
65 parsing (see: --pretty below).
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68 Most arguments have short and long forms. The long forms are more
69 likely to be stable over time, and hence should be used in scripts
70 which call ipcress.
71 -h | --shorthelp <boolean>
73 Show help. This will display a concise summary of the available
74 options, defaults and values currently set.
75 --help <boolean>
77 This shows all the help options including the defaults, the
78 value currently set, and the environment variable which may be
79 used to set each parameter. There will be an indication of
80 which options are mandatory. Mandatory options have no default,
81 and must have a value supplied for ipcress to run. If mandatory
82 options are used in order, their flags may be skipped from the
83 command line (see examples below). Unlike this man page, the
84 information from this option will always be up to date with the
85 latest version of the program.
86 -v | --version <boolean>
88 Display the version number. Also displays other information
89 such as the build date and glib version used.
90
92 -i | --input <path>
93 PCR experiment data in the ipcress file format described above.
94 -s | --sequence <paths>
96 Specify the sequences. Multiple files may be specified here,
97 which reduces the FSM building overhead, and makes ipcress run
98 faster than running the process separately.
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101 -m | --mismatch <mismatches>
102 Specify the number of mismatches allowed per primer. Allowing
103 mismatches reduces the speed of the program as a large primer
104 neighbourhood must be constructed, and fewer experiments can be
105 fitted in memory prior to each scan of the sequence databases.
106 -M | --memory <Mb>
108 Specify the amount of memory the program should use. The more
109 memory made available ipcress, the faster it will run, as more
110 PCR experiments can be conducted in each scan of the sequence
111 databases. This does not include memory used during the scan
112 (for storing partial results and sequences), so the actual
113 amount of memory used will be slightly higher.
114 -p | --pretty <boolean>
116 Display results in a human-readable format, not designed for
117 parsing.
118 -P | --products <boolean>
120 Display PCR products as a FASTA format sequence.
121 -S | --seed <length>
123 Specifiy the seed length for the wordneighbourhood for the FSM.
124 If set to zero, the full primer is used. Shorter words reduce
125 the size of the neighbourhood, but increase the time taken by
126 ipcress to filter false positive matches.
127
129 Not documented yet.
130
132 ipcress test.ipcress sequence.fasta
133 This is the simplest way that ipcress can be used.
134 ipcress dbsts_human.ipcress --sequence ncbi30/*.fasta --mismatch 1
135 Compare a input file against a set of fasta files, allowing one
136 mismatch in each primer.
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139 This documentation accompanies version 2.2.0 of the exonerate package.
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142 Guy St.C. Slater. <guy@ebi.ac.uk>. See the AUTHORS file accompanying
143 the source code for a list of contributors.
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146 This source code for the exonerate package is available under the terms
147 of the GNU general public licence.
148 Please see the file COPYING which was distrubuted with this package, or
150 http://www.gnu.org/licenses/gpl.txt for details.
151 This package has been developed as part of the ensembl project. Please
153 see http://www.ensembl.org/ for more information.
154
156 exonerate(1),e-PCR
157ipcress March 2003 ipcress(1)