Description:
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- FPMiner is a professional, cross-platform software tool for fully
automated high-throughput processing of capillary
fingerprinting data for physical mapping or genomic research
projects.
- FPMiner provides the accurate peak finding algorithms and
peak size calling algorithms to size DNA fragments of capillary
fingerprinting samples. The sized fragment data can be used
for further genotyping or fragment analysis.
- FPMiner uses automated fingerprint editing algorithms to
remove undesired fragments, and exports the FPC-ready
fragment size files for further contig assembly.
- Users can quickly check the accuracy and the quality of capillary
run and fingerprint editing with size matching quality score
(SMQS) and fingerprint editing quality score (FEQS).
- FPMiner has a built-in database and support MySQL database,
and can process large number of samples.
- FPMiner can check plate orientation errors and screen and
remove cross-contamination and chloroplast or/and
mitochondrial DNA contamination.
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Key Features:
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- Cross platform support: Support Windows (95/98/2000/XP/NT,
etc), Unix/Linux and Mac OS X, and any other systems that can
run Java applications.
- Support multiple input data formats: Four major data formats
are supported: raw sample file (.fsa) from ABI slab gel or
capillary instruments, GeneMapper output file (.gm) which is the
output from FPPipeliner software (BioinforSoft, Beaverton, OR,
USA) and GeneMapper software (Applied Biosystems, Foster
City, CA, USA, SCF files from MegaBACE capillary systems and
BaseStation Analyzer, and FPC size file (.sizes or .bands) which
is compatible with FPC software (Soderlund et al., 1997,
Soderlund et al., 2000).
- Support multiple concurrent projects: Multiple projects based
on built-in databases or MySQL databases can be created for
different fingerprinting data. Each project can accommodate up
to 20,000 samples. All samples and analyzed results can be
easily edited, queried and exported using data manager and
editing tools.
- Batch processing of fingerprint profiles: Based on the
proprietary algorithms, FPMiner can automatically perform
fragment size-calling and remove unwanted fragments from
fingerprint profiles. All edited fragment size information is saved
in the project database and can be further edited, analyzed, and
exported. The hundreds of thousands of fingerprinted samples
in multiple projects can also be batch-processed in a pipeline
automatically without human's attention.
- Capability of manually editing of fingerprint data: Multiplex
chromatograms can be viewed graphically. All fragments in a
profile can be freely edited by changing threshold of peak height
or deselecting a fragment.
- Capability of quality control: FPMiner provides a quality control
system that includes trace quality score for each fingerprint
plate, size calling quality score, and fingerprint profiler editing
quality score for each fingerprint sample. These scores will
help scientists to evaluate the fingerprinting quality and data
analysis quality to achieve high quality analysis results in a
high-throughput manner.
- Capability of experimental error check and DNA contamination
check of BAC clones: FPMiner proides analysis tools to check
and correct plate orientation errors, to screen and remove
cross-contaminated clones, and screen and remove
chloroplast DNA (for plant) and/or mitochondrial DNA
contaminated clones.
- Statistical analysis of edited fragments: Histogram (frequency
distribution) and basic statistics of the edited fragments and
quality scores of samples can be calculated based on all the
samples of a project or part of the samples selected by a user.
- Removal of fragments generated from vector and high
frequency fragments by fragment frequency analysis: If a
fragment was repeatedly sized by electrophoresis, the
observed sizes will be normally distributed from which a
standard deviation can be assessed and will serve as the base
of tolerance determination for further contig assembly with FPC
software (Soderlund et al., 1997, Soderlund et al., 2000). From
a set of fingerprinting profiles, empirical data of sizes of vector
fragments, or high frequent fragments can be assessed, and
those fragments can be removed from data set as you wish.
- Capability of viewing fingerprint patterns in a gel manner: The
fingerprint profiles of the edited fragments can be viewed as a
virtual gel image.
- Convenient data export: FPMiner can export filtered and edited
fragment data into FPC-ready size files that can be directly used
in down-stream contig assembly with FPC software (Soderlund
et al., 1997, Soderlund et al., 2000). The edited fragment data,
such as peak size, peak height, peak area, peak scan number,
etc. of clones or DNA samples can be also exported in a text
format.
- Support commanline commands. FPPipeliner 3.0 includes
FPMiner 1.4 or hiher version as a sizing software and perform
high-throughput fragment sizing of samples. See FPPipeliner
user's guide for details.
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Requirements:
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- Java running environment: J2SE or JRE 1.4 or above: FP Miner
has a bundle with JRE.4.2.
- Minimum requirements:
- Pentium III processor for Windows or Linux, and G4
processor and Mac OS X for Mac.
- 512 MB of memory
- 10 GB free disk space
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Installation:
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- Download the FPMiner software
- In Windows and Mac OS X, double-click the FPMiner installer
(self-extracted executable file) and just follow the instructions to
install the software.
- In Unix/Linux, type the full name of installer and press return
key, and follow the instructions to install software.
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