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The Fingerprint Types module
A fingerprint is defined as any densitometric record seen as a profile of peaks or bands. Examples are electrophoresis patterns (gel, capillary), gas chromatography or HPLC profiles, spectrophotometric curves, MALDI, SELDI, etc.
 Since electrophoresis is an important technique in studying relationships in biology, BioNumerics offers comprehensive tools for preprocessing electrophoresis fingerprints. These tools include reading graphical and densitometric file formats from image files and automated sequencers, lane finding, normalization (alignment of patterns), band finding and quantification, band matching, etc.
In addition to the wide range of analysis functions for fingerprint data, BioNumerics provides comprehensive tools for automated preprocessing and analysis of specific fingerprint types such as MALDI, dHPLC, and chromatogram files from automated sequencers. The software also offers a number of specialist plugins for electrophoresis-based applications such as VNTR or MLVA, HDA or CSCE, spa-typing, AFLP-based breeding, etc. Through its easy and powerful script language, BioNumerics can import and process virtually any type of fingerprint data from any manufacturer.
Specifications:
Image processing and normalization. Input of any bitmap images, densitograms, and chromatograms of unlimited file size. Image pre-editing and cleaning. 3D representation of bitmaps. Automatic lane finding for all types of gels. Gelstrip borders and tracking splines adjustable for individual lanes. Automated and manual alignment by pattern recognition using external reference patterns and/or internal reference bands. On-screen normalization of bitmap images with indication of reliability and possible misalignments. Direct processing of sequencer chromatogram files and fragment analysis files with inline reference tracks. Adjustable background subtraction and curve smoothing. Spot removal. Display of any combination of normalized 2D-bitmap strips, densitograms or reconstructed patterns. Direct comparison of patterns normalized with different reference systems.
Quantification. Band-search algorithms with adjustable sensitivity for shoulder and double-band finding. Possibility to find and mark uncertain bands/peaks. Quantification of molecular sizes or any other metric unit using linear, logarithmic, combined logarithmic-third power regression, cubic spline or pole functions. Accurate expression of protein or nucleic acid quantities or concentrations based on cubic spline regression using known calibration peaks. Comparative quantification of bands/peaks between groups of patterns. Generation of tables and reports for unlimited numbers of patterns, indicating molecular weight, fragment length, absence/presence or absolute amounts of protein or DNA per band/peak. Search for discriminative bands/peaks between selected groups of patterns; search for unique and common bands/peaks. Binary and quantitative band matching tables of multiple combined fingerprints. Possibility to define named band classes based upon size and position (e.g. for DGGE/TGGE analysis). Add/edit bands directly in the comparison window in band matching mode.
Error values. Import data from high-throughput molecular fingerprint techniques (such as MALDI, SELDI,...) with error values (e.g. standard deviations). Show errors in the curve window or compare them with an error-weighted correlation coefficient.
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Bioanalysis made easy
