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GFS / Genome-based Fingerprint Scanning
Predicts the genomic origins of proteins by scanning their peptide-mass fingerprints against an entire genome, subjected to translation and trypsin digest in silico. The GFS program uses the experimentally obtained peptide-mass fingerprint as input, and outputs the most likely regions of the genome from which the mass fingerprint is derived. The GFS method has promise for identifying proteins involving nonstandard translation and also has potential to be used for genome annotation based directly on observed proteins.
AFLPinSilico / Amplified Fragment Length Polymorphism in Silico
Mimics amplified fragment-length polymorphism (AFLP) experiments and produces virtual fingerprints that enable the identification of fragments. AFLPinSilico performs AFLP simulations with different combinations of restriction enzymes or selective nucleotides, on organisms or data sets for which DNA sequences are available. The software also allows to follow bands over different experiments or over a time-course. It can be applied for producing cDNA-AFLP results and for testing restriction enzymes as well as digestions of bacterial artificial chromosome (BAC) sequences.
ANATool / Arabidopsis Natural Accession Tool
Provides dynamic access to the fingerprints and genotypes of the accessions. ANATool provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology. It is composed of two tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions.
GELect
An image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. GELect was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. This tool can accurately segment lanes from a gel matrix, intelligently extract distorted and even doublet bands that are difficult to identify by existing image processing tools. Consequently, genotyping from DNA gel electrophoresis can be performed automatically allowing users to efficiently conduct large scale DNA fingerprinting via DNA gel electrophoresis.
Genome Fingerprints
Summarizes personal genomes that does not require knowledge of the technology, reference and encoding used, and yields “genome fingerprints”. Genome Fingerprints rapidly computes the level of similarity between genomes regardless of representational differences. It is a fully deterministic form of locality-sensitive hashing and can be applied to large-scale sequence comparisons, protein classification, metagenome clustering, and detection of gene–gene interactions.
AQ / Advanced Quantifier
A software system for analyzing scanned images of protein or DNA samples run in one-dimensional separations, including northern, Southern and western blots, RAPDs, STRs, paternity and forensic analysis using RFLPs or STRs, strain identification and comparison using RFLPs or STRs, and other genetic mapping applications using 1-D molecular techniques. AQ automatically locates lanes and bands. On command, it determines band size and quantity of sample present in comparison to standards or reference lanes.
MI Software / Molecular Imaging Software
Provides high performance image analysis for a wide range of molecular imaging applications. Featuring a comprehensive set of tools for quantitation, image display, databasing, and reporting, MI Software improves the quality and ease of image analysis for in vivo and ex vivo samples such as small animal tissue, plates and more. An intuitive navigational structure featuring workflow driven tool palettes further streamlines the optimization and analysis of images.
Quantity One 1-D
It can acquire, quantitate, and analyze a variety of data, including radioactive, chemiluminescent, fluorescent, and color-stained samples acquired from densitometers, storage phosphor imagers, fluorescence imagers, and gel documentation systems. Quantity One 1-D allows automatic configuration of these imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. Its flexible tools allow automated analysis of 1-D electrophoretic gels, western blots, dot blots, slot blots, arrays, and colony counts for fast, high-quality results.
Gel-Quant
Analyses one dimensional gel images. After electrophoresis, scan your gel image into a bitmap format. Once the image is digitized, use Gel-Quant to provide mass and molecular weight analysis, automatically locate the lanes on the gel image, automatically straighten curved and distorted lanes, select an area of interest from the image for further processing, graphically present each lane profile separately or overlay lanes of interest, perform Gaussian curve fitting for bands within lanes, schematically present the processed bands, arrange data from calculations made on the processed gel into a data table and convert gel images from negative to positive. Results of the entire process, including the original image and analysis data, can be stored and printed. Results can also be exported in several common formats.
GelAnalyzer
Allows one to analyze gel images obtained by a scanner, camera, or digital camera and ensures the visual control of the identification and comparative analysis of bands; it also makes it possible to take into account the bands that are poorly identified automatically and exclude the artifacts (incidental marks) on images. The operation of "GelAnalyzer" software is based on the determination of the values of normalized coordinates of bands with allowance for the relative electrophoretic mobility (Rf) of PCR products and comparison of their spectra (set of bands in gel lanes) to reveal the similarities or differences in their components with subsequent statistical data processing and display the results of the analysis.
BDA / BioDocAnalyze
A powerful package of imaging and analysis software supporting different camera models. The software tool provides sample analysis of electrophoresis gels and blots with best results in a minimum amount of time. BDA can be used for fluorescent, colorimetric and chemiluminescent applications and accepts typical file formats like JPG, TIF, and BMP. Gel images can be directly transferred from the image acquisition window of BDAdigital or BDA live to the analysis software window. Also files generated with other acquisition sources can be imported.
GelQuant.NET
An image analysis, processing and quantitation program. For standard JPEG, BMP, PNG, TIFF images. It is easy to magnify, zoom, rotate by any angle, flip, evaluate overexposure, adjust brightness, contrast, invert and save images. Intensity of a band or an image segment is quantified by drawing a selection rectangle and pressing the middle button of a mouse. Absolute intensity, local average-corrected intensity and % of the signal over total signal across several areas are computed.
myImageAnalysis
Obsolete
A full-featured, multifunction computer program to analyze and edit digital images of electrophoresis gels and blots that were acquired using gel documentation imagers or scanners. The main functions include intuitive design, compatible file types, image comparison, auto-identification, MW determination, advanced quantitation, image refinement and annotation and sharing. myImageAnalysis comprises a complete set of easy-to-use research tools for the quantitative digital analysis of image data from electrophoresis gels and western blots.
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