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Extensions

Introduction

This is a list of available extensions to the ProbeMaker framework.

These types of extensions, or plug-ins, are possible:

List of extensions

The following is a list of available extensions, grouped by extension types. Some of these extensions are included in the distribution of the package.


Target types

Circularization target

Class name:
org.moltools.apps.probemaker.ext.target.
CircularizeTarget
Description:
This target type will generate a probe that functions as a template for circularization of the target
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Gap-fill padlock target

Class name:
org.moltools.apps.probemaker.ext.target.
GapFillPadlockTarget
Description:
Generates a Gap-fill padlock probe for the target. May be targetted against a SNP in the sequence
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Minisequencing target

Class name:
org.moltools.apps.probemaker.ext.target.
MinisequencingTarget
Description:
Generates a minisequencing primer for either strand of the target (both strands if expanded). SNPs in the sequence may be targetted. No 5' TSS generated.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Padlock probe (allele-specific) target

Class name:
org.moltools.apps.probemaker.ext.target.
PadlockTarget
Description:
Generates allele-specific padlock probes for SNP targets. Expand targets to group the allelic variants. May also target a specified position of the target (no allele-discrimination)
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Selector target

Class name:
org.moltools.apps.probemaker.ext.target.
SelectorTarget
Description:
Generates selector probes. Position for structure-specific cleavage should be indicated by a '|'
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Whole sequence as template

Class name:
org.moltools.apps.probemaker.ext.target.
UnchangedTarget
Description:
Generates a single TSS that is complementary to the whole target sequence
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Input file formats

Fasta format

Class name:
org.moltools.apps.probemaker.ext.dbif.
FastaFormat
Description:
One or more sequences in fasta format:
>name of sequence 1
sequence data for sequence 1 on one or more lines
>name of sequence 2
sequence data for sequence 2...
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

PieceMaker output format

Class name:
org.moltools.apps.probemaker.ext.dbif.
PieceMakerFormat
Description:
Sequences from a PieceMaker output file
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Text table format

Class name:
org.moltools.apps.probemaker.ext.dbif.
TextTableFormat
Description:
One or more sequences in tab-, semi-colon-, or comma-delimited text table format:
name of sequence 1[TAB]sequence
name of sequence 2[TAB]sequence
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Sequence converters

Change SNP notation: (C/G) -> C/G

Class name:
org.moltools.apps.probemaker.ext.conv.
ParanthesesConverter
Description:
Converts from (C/G) notation to C/G notation supported by ProbeMaker
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Change SNP notation: [C/G] -> S

Class name:
org.moltools.apps.probemaker.ext.conv.
PlugInBracketsToDegeneracyConverter
Description:
Converts from [C/G] notation to degenracy code (S in this case), which is supported by ProbeMaker
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Target database builders/modifiers

Select first bi- or tri-allelic polymorphism

Class name:
org.moltools.apps.probemaker.ext.dbb.
FirstBiAllelicSelector
Description:
Selects the first variant with two or three options in the target sequence
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Select the first variant of each target

Class name:
org.moltools.apps.probemaker.ext.dbb.
FirstVariantSelector
Description:
Selects the first variant of the target sequence
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Analysis modules

Hybridization interference

Class name:
org.moltools.apps.probemaker.ext.mod.
DefaultHybInterferenceModule
Description:
Determines whether the sequence adjacent to the target-specific sequences will interfere with the intended hybridization by extending the hybrid by one or more bases.
This is done by comparing performing a Smith-Waterman alignment of the TSS + adjoining sequence and the corresponding part of the target.
If the strongest alignment found is longer than the TSS, a hybridization interference message is given.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Tag sequences outside of intended positions

Class name:
org.moltools.apps.probemaker.ext.mod.
DefaultTagOccurrenceModule
Description:
Determines if the sequence of any tag occurs outside the intended position. Also check if the complement of any tag occurs outside the intended position. If the max score parameter is set to 100, a full match string search is performed, if the parameter is set to less than 100, a Smith-Waterman alignment is performed, and a match is called if the alignment score exceeds the limit defined as the alignment score for a full match * the per cent limit. If a match is scored outside of the intended position, an error message is given.
If the tag sequences or their complements are specifically allowed to occur by the Tag settings, the corresponding tests are not performed.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Dummy module

Class name:
org.moltools.apps.probemaker.ext.mod.
DummyModule
Description:
Dummy module that adds warning message to candidates by chance
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

False priming

Class name:
org.moltools.apps.probemaker.ext.mod.
FalsePrimingModule
Description:
False priming according to the algorithm described in:

Kaderali et al. (2003) Primer-design for multiplexed genotyping. Nucleic Acids Res., 31, 1796-1802.

The four 3'-terminal nucleotides of the primer/probe (3'TSS) are matched to each target sequence. If a match is found (except at the position of the intended priming site) an alignment is performed between the primer and the target at that position. If the Tm of the strongest alignment is above the limit, an error message is given. Tm is calculated as described in:

Leber et al. (2005) A fractional programming approach to efficient DNA melting temperature calculation. Nucleic Acids Res., 31, 1796-1802.

Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

GC content module

Class name:
org.moltools.apps.probemaker.ext.mod.
GCContentModule
Description:
This module limits % GC content in the target sequence.
Author:
Magnus Isaksson
Comments:
This extension is included in the ProbeMaker package

Gap-fill padlock probe ligation

Class name:
org.moltools.apps.probemaker.ext.mod.
GapFillPadlockLigationModule
Description:
Checks if a gap-fill padlock probe will template the ligation of itself or of another probe in the set. This is done by checking the 5' and 3' terminal nucleotides of the probe and searching for the complement of this sequence in the other probe. The number of bases required to match on either side is speicified by two parameters.
An error message is given if a matching sequence is found. A gap of one base is allowed between the two 5' and 3' sequences.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Gap-fill padlock TSS ligation

Class name:
org.moltools.apps.probemaker.ext.mod.
GapFillPadlockTSSLigationModule
Description:
Checks if a gap-fill padlock probes will be templated for ligation by another target in the set or by another probe in the probe set. Also checks if the probe will be templated for ligation by another part of its own target.
This is done by checking the 5' and 3' terminal nucleotides of the probe and searching for the complement of this sequence in the other probe. The number of bases required to match on either side is speicified by two parameters. A gap of one nucleotide is allowed between the 5' and 3' sequences.
An error message is given if a matching sequence is found.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Padlock probe ligation

Class name:
org.moltools.apps.probemaker.ext.mod.
PadlockLigationModule
Description:
Checks if a padlock probe will template the ligation of itself or of another probe in the set. This is done by checking the 5' and 3' terminal nucleotides of the probe and searching for the complement of this sequence in the other probe. The number of bases required to match on either side is speicified by two parameters.
An error message is given if a matching sequence is found.Optionally, the Tm of the probe-target hybrid should also exceed a given limit. Tm is then calculated by the algorithm described in:

Leber et al. (2005) A fractional programming approach to efficient DNA melting temperature calculation. Nucleic Acids Res., 31, 1796-1802.

Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Padlock TSS ligation

Class name:
org.moltools.apps.probemaker.ext.mod.
PadlockTSSLigationModule
Description:
Checks if a padlock probe will be templated for ligation by another target in the set or by another probe in the probe set. Also checks if the probe will be templated for ligation by another part of its own target.
This is done by checking the 5' and 3' terminal nucleotides of the probe and searching for the complement of this sequence in the other probe. The number of bases required to match on either side is speicified by two parameters.
An error message is given if a matching sequence is found.
Optionally, the Tm of the probe-target hybrid should also exceed a given limit. Tm is then calculated by the algorithm described in:

Kaderali et al. (2003) Primer-design for multiplexed genotyping. Nucleic Acids Res., 31, 1796-1802.

Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Probe length

Class name:
org.moltools.apps.probemaker.ext.mod.
ProbeLengthModule
Description:
Checks if the probe is of the preferred length as specified by the Spacer settings.If not, an error message is given.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Selector probe ligation

Class name:
org.moltools.apps.probemaker.ext.mod.
SelectorLigationModule
Description:
For use in TSS evaluation stage.
Checks if a selector probe will ligate to another target in the set or to another selector in the set. If structure-specific cleavage is used, also checks if the probe will be ligated on the 5' end of its own target.
Also checks if selector will ligate to itself.
Tests are done by checking the 5' or 3' terminal nucleotides of the appropriate sequence and checking if they occur at the potential ligation site.The number of bases required to match is speicified by parameters.
An error message is given if a matching sequence is found.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Sliding window heterodimer formation module

Class name:
org.moltools.apps.probemaker.ext.mod.
StringHeteroDimerModule
Description:
Tests whether a probe will form a dimer with another probe by searching
for complementary substrings by a sliding window approach
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

TSS length and temperature module

Class name:
org.moltools.apps.probemaker.ext.mod.
TSSLengthAndTmModule
Description:
Determines whether the target-specific sequences are within the limitsof length and temperature.
If temperature is outside of the allowed span, but inside twice that span, a warning is given, if outside the double span, an error message is given. If length is outside of the allowed range, an error message is given.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Tag allocation

Class name:
org.moltools.apps.probemaker.ext.mod.
TagAllocationModule
Description:
Checks if all tags have been allocated. If there are too few tags in one or more of the tag libraries, the allocation will fail.
If all tags have not been allocated, a fatal message is given.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Tm-based dimer formation module

Class name:
org.moltools.apps.probemaker.ext.mod.
TmProbeDimerModule
Description:
Tests whether a probe will form a dimer with another probe by performing a Tm calculation with the fractional programming approach described in

Leber et al. (2005) A fractional programming approach to efficient DNA melting temperature calculation. Nucleic Acids Res., 31, 1796-1802.

Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Probe acceptors

Accept all TSS pairs and candidates

Class name:
org.moltools.apps.probemaker.ext.acc.
AllAcceptor
Description:
Accepts all presented TSS pairs and candidates
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

User accepts through GUI

Class name:
org.moltools.apps.probemaker.ext.acc.
GUIAcceptor
Description:
Prompts the user to accept or reject candidate. Use with caution.
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Accept Good candidates. Two-member groups accepted in group.

Class name:
org.moltools.apps.probemaker.ext.acc.
GoodAcceptor
Description:
Accepts candidates of best quality only, uses pair-wise acceptance when applicable
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Accept Good candidates, Fair ones for selection

Class name:
org.moltools.apps.probemaker.ext.acc.
GoodFairAcceptor
Description:
Accepts candidates of highest quality directly, while candidates of intermediate quality are temporarily stored
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Good accepted, fair temporarily. Max number of candidates per probe.

Class name:
org.moltools.apps.probemaker.ext.acc.
MaxNumberAcceptor
Description:
Limits the total number of candidates evaluated per probe
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Probe selectors

Select probe with best quality

Class name:
org.moltools.apps.probemaker.ext.sel.
BestQualitySelector
Description:
Selects the highest quality probe
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Select first candidate in list

Class name:
org.moltools.apps.probemaker.ext.sel.
DefaultProbeSelector
Description:
Selects the probe accepted first
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

User selects

Class name:
org.moltools.apps.probemaker.ext.sel.
GUISelector
Description:
Prompts the user to select probe (use with caution)
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

No selection

Class name:
org.moltools.apps.probemaker.ext.sel.
NoSelector
Description:
Performs no selection (last accepted will be used)
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Probe output formats

FASTA format

Class name:
org.moltools.apps.probemaker.ext.pof.
FastaOutputFormat
Description:
Outputs probe sequences in fasta format
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

HTML Format

Class name:
org.moltools.apps.probemaker.ext.pof.
HTMLOutputFormat
Description:
Outputs detailed probe information in fasta format
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Semi-colon delimited

Class name:
org.moltools.apps.probemaker.ext.pof.
SemiColonDelimitedOutputFormat
Description:
Outputs probe sequences on one line each, lines ending with semi-colon
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Tab delimited text table w. target info

Class name:
org.moltools.apps.probemaker.ext.pof.
TargetInfoTextTablePOF
Description:
Outputs probes in text table format with some target info appended
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package

Tab delimited text table

Class name:
org.moltools.apps.probemaker.ext.pof.
TextTableOutputFormat
Description:
Outputs probes in text table format
Author:
Johan Stenberg
Comments:
This extension is included in the ProbeMaker package