DNA Methylation Analysis, Bisulfite Sequencing

CpGviewer (University of Leeds, UK)

Sequencing of cloned bisulphite-modified DNA is a widely-used method for analysis of genomic methylation. Although straightforward in principle, in practice the data manipulation can be involved and time consuming.

CpGviewer is a free computer program that aims to be a simple integrated tool for handling bisulphite sequencing projects. It can process plain text sequences or electropherogram trace files (.ab1 files from Sequencing Analysis Software) from Applied Biosystems Genetic Analyzer instruments and allows interactive editing of the sequences, aligned to a reference sequence. It provides methylation specific data analysis and visualization. It also offers the facility to generate figures for publication and to design primers for bisulphite-treated templates.

		Supports both raw or base called data
		Generates a bisulfite converted reference sequence from a non-converted input and identifies CpG's
		Batches a large number of files, and assembles the data
		Methylation specific visualization

Intended Users: Anyone who works with DNA methylation data from bisulfite sequencing; occasional users as well as experts

DNA Methylation Analysis, Bisulfite Sequencing

BiQ Analyzer (Max Planck Institute for Computer Science)

BiQ Analyzer is a free software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing.

		End-to-end support of the analysis process: from raw sequence files to comprehensive documentation and visualization
		Automatical generation of publication-quality 'lollipop diagrams'
		Integrated 1-click multiple sequence alignment
		Automated CpG highlighting
		Factor 5 speedup over manual analysis, plus systematic quality control

Intended Users: Anyone who works with DNA methylation data from bisulfite sequencing; occasional users as well as experts (beginners will benefit from help with quality control whereas experts will save hours and days of tedious work by using BiQ Analyzer).

Web-based Diagram Generation: Diagram generation is also available as a web service for users who analyze their DNA methylation data outside BiQ Analyzer but want to generate high-quality 'lollipop diagrams' directly.

DNA Sequencing, Fragment Analysis, Genotyping, Data Management, LIMS

Finch® Suite Software (Geospiza)

Commercial Off-the-shelf software for genetic testing for contract core labs, life science research labs, molecular diagnostic labs and bio-therapeutic manufacturing labs to manage and automate the production and analysis of genetic data.

The Genetic Analysis Integration Tool links the Finch Suite LIMS with the Applied Biosystems GeneMapper® Software v4.0 and SeqScape® v2.5 software applications.

Genotyping

Exempler for Genotyping
(Sapio Sciences LLC)

Advanced genetic analysis tool for modeling the genetic roots of disease. Exempler includes:

ABI File Import Wizard: Import GeneMapper® data. Supports ABI's hCV naming convention as well as RS'id SNP identifiers.

Complete Statistical Analysis: Calculate statistics such as QLT, TDT (family based), LD, Chi Square, Fishers, Odds Ratio LOH, and Haplotype analysis (EM algorithm) for association studies.

Gene Ontology Module: Map significant SNP's to their related ontological information in support of functional genomics research.

Genetic Algorithm Module: Discover multi-loci models that correspond with phenotypes.

Extensive Annotations: Includes DbSNP, Human Gene and Gene Ontology. Automatic calculation of related genes based on user definable SNP-to-gene base pair distance.

Resequencing, MLPA, HLA typing

Sequence Pilot (JSI Medical Systems)

Sequencing: Patient-based mutation detection, easily configurable for any gene, high degree automation and security for high-throughput DNA sequencing.

HLA: Sequencing-based typing (SBT) for HLA with generic and allele specific result calculation in different resolutions (2-digit and 4-digit, maximum resolution).

MLPA: Configurable for any MLPA kit; variable analysis modes; automated peak assignment with electropherogram view and result display.

Sequence analyses

CLC Combined Workbench
(CLC bio)

CLC Combined Workbench features a number of unique and innovative bioinformatics tools for supporting advanced biochemistry and molecular biology lab research within DNA, RNA and proteins.

• Sequence data analyses
• Alignments
• Assembly
• Primer design
• Molecular cloning
• Advanced RNA structure prediction and editing
• Secondary protein structure predictions

Cross-platform
CLC Combined Workbench is cross-platform, functioning on Mac OS X, Windows, and Linux.

Intended users
Bioinformaticians and molecular biologists alike can gain numerous advantages by using the integrated environment provided with this workbench.