Mutation Surveyor® Sequence analysis and assembly software… utilizes our patent pending physical trace comparison technology which provides accuracy >99% when using bi-directional Phred 20 quality sequence traces. The software is an excellent tool for both discovery and diagnostic applications, and accepts sequence traces from all major sequencing systems such as those marketed by Applied BioSystems, Foster City CA, Beckman Coulter or MegaBACE systems, and is compatible with either terminator or primer chemistries. The software’s unique technology provides the best tool for locating all DNA variants: Homozygote, Heterozygote, Indels and heterozygote insertions or deletions.

Features:

• High Sensitivity
• >99% Accuracy
• Automatic Het-Indel De-convolution
• Automated Methylation Analysis & Quantification
• Hypervariable Region Detection
• Sequence Assembly
• Base Calling and Correction
• Custom Report Creation
• Clinical Report formats
• Validated for use in clinical sequence analysis by NGRL, UK & UPMC

SoftGenetics’ NextGENe software, is a unique program for analyzing “Next Generation” Sequencing data, generated by all of the new platforms.  

NextGENe’s “Biologist Friendly” user interface combined with its speed and unique algorithms allows analysis on low-cost 64 bit hardware.  NextGENe’s simplicity and powerful algorithms backed by SoftGenetics world class technical support nearly eliminates the need for additional bioinformatics resources. 

Multiple Applications:

NextGENe is a software suite designed to allow biologists to easily analyze the vast amount of data generated by “Next Generation” Sequencing systems, NextGENe provides an intuitive Windows® user interface and a host of applications including:

• de novo and target assembly
• SNP/Indel Discovery
• Digital Gene Expression Studies    
• Transcriptome with cDNA
• ChIPSeq
• miRNA Discovery/Quantification. 
  

Benefits:

• Low end computer requirements
  - NextGENe significantly reduces capital costs by utilizing low-cost Windows® 64 bit hardware.
• Easy-to-use
  - Windows format and data-in, results-out interface speeds analysis while significantly reducing user interface requirements.
• Low Bioinformatics costs
  - Preprogrammed applications drastically reduce need for bioinformatics personnel.

Biologist-friendly interface eliminates need for high level computer skills. 

Compatibility:

NextGENe provides cross instrument platform compatibility.
All applications are tailored to accept data from:

• Illumina® Genome Analyzer
• Roche Genome Sequencer FLX™
• Applied BioSystems SOLiD™ System
• Helicos Biosciences (in development)

GeneMarker® the “Biologist Friendly” genotyping software… is an excellent replacement for GeneScan®/GenoTyper® or an easy-to-use alternative to GeneMapper®. GeneMarker’s basic operation is simple, fast and accurate. GeneMarker is compatible with all major electrophoresis systems including Applied Biosytems PRISM™ Genetic Analyzer, MegaBACE™, Beckman-Coulter and SpectruMedix systems. When used in combination with JelMarker™ GeneMarker is an excellent choice for analysis of any gel image from systems such as the LI-Cor® 4300 DNA analyzer or Kodak Image Station 4000R.

Features:

• Automated Correction of most chemistry & instrumental errors
• Biologist Friendly interface & graphics
• Report Customization
• User Management

Integrated modules for:

GeneMarker®HID STR Human Identity Software… is an excellent replacement or alternative to GeneScan/Genotyper or GeneMapperID. Collaborator comparison studies have indicated analysis time savings of over 25% in direct comparison to GeneMapperID. Developed in collaboration with the Pennsylvania State University Forensic Science program GeneMarkerHID is an excellent tool for casework, paternity and all other human identity applications such as stem cell research and identification.

Features:

• Unique Pattern recognition and sizing technology provides >99% Accuracy
• Easy Linked Navigation
• Management Control and tracking
• Instrument Compatibility: ABI, MegaBACE, Beckman-Coulter
• Compatible with major STR kits, including Cofiler,®, Profiler®, Identifiler®, Minifilier®
• SGMPlus®,PowerPlex®16
• Optimized to analyze profiles from Y-STRs & LCN samples
• Individual Peaks are Quality Flagged
• Relationship Testing Feature
• Supervisor Review Module
• Exportable CODIS and LIMS Reports
• Bulk Printing Capabilities
• Student/Instructor module available

JelMarker™ image reading and conversion software…was developed in response to a growing demand for software that can analyze fluorescence, chemiluminescence and autoradiography gel image files – especially those from LI-COR’s 4300 DNA Analyzer and KODAK’s Image Station 4000R.

JelMarker™ is a simple, stand-alone image reading software providing highly accurate lane and band recognition. Easy-to Use, modern Windows technology permits rapid point and click modification to lane and band positions.

• Highly accurate lane and band recognition
• Easy to modify lane and band positions using a point-and-click methodology
• Export two color images in SCF format for fragment analysis

Applications:

AFLP
Microsatellite
TILLING®
EcoTILLING®
SNP discovery

JelMarker™ can import up to two TIFF, BIP, JPEG, and TXT files for simultaneous analysis.

JelMarker™ exports SCF files for easy upload to GeneMarker® for highly accurate, sensitive and rapid analysis.

CGH Explorer™ Comparative Genome Hybridization software… utilizes genomic DNA from both reference and test genome that are labeled with fluorescent dyes. The genomic samples competitively hybridize with an array of probes arranged on a substrate. The hybridized slide can be scanned evaluating the signal intensity ratio for the two dyes to determine the copy number for each DNA segment. The majority of microarray platforms use short DNA fragments (25– 75 base pairs), oligonucleotides, or larger BAC clones of about 100 kbp. Along with the arrays covering chromosome specific regions, there are genome wide arrays used for quick assessment of losses and gains in larger regions. In addition, cDNA arrays, originally designed for gene expression profiling, are used to evaluate the number of copies in coding regions.

CGH Explorer™ is an easy-to-use software tool for analyzing two color copy number alteration arrays from multiple platforms, including AgilentTechnologies, Illumina, AffyMetrix, NimbleGen, BioRobotics, Combimetrix and others.

The software performs raw image analysis and gridding eliminating image biases to significantly improving analysis accuracy. Simple, user-friendly interface and automation features speed analysis providing final results within a few mouse clicks.

Features:

• Multiple Platform Compatibility
• Raw Image Processing improves accuracy and precision
• Comparative Analysis of multiple projects
• Automated parameter setting
• Integrated from raw image processing through final reporting of results
• Batch Processing Capability
• Rapid Analysis performed in minutes
• Easy-to-Use Windows interface
• Multiple Quality Control functions