Extensions
Introduction
This is a list of available extensions to the ProbeMaker framework.
These types of extensions, or plug-ins, are possible:
- Target types
- File formats
- Sequence converters
- Target database builder/modifiers
- Analysis modules
- Acceptors
- Selectors
- Probe output formats
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