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Genchek™

Genchek™ is a comprehensive, multi-platform, sequence analysis software package. It facilitates analysis of Expressed Sequence Tags (ESTs), Complete Genome, and SNP (Single Nucleotide Polymorphism) data. Genchek™ is a research information and experiment management tool that integrates public and proprietary data through a discovery workspace that provides contextual access to sequence analysis tools, content and services. Genchek™ has an integral database system that can be used to access, store, organize and retrieve DNA, protein and vector sequences in an intuitive environment that offers editing, management and annotation of sequences.

Integrated Sequence and Graphical Viewer
• Sequence as single strand, double strand, translation and with annotations.
• Publication quality circular and linear sequence maps in our graphical viewer.
• Graphical view of restriction maps that facilitates easy cloning.
• Graphical view of ORFs in the sequence maps.
• Imported and user defined sequence annotations in graphical and sequence views.

BLAST Suite
• Supports blastn, blastp, blastx, tblastn, tblastx and Batch Blast.
• Create customized local BLAST databases through our pluggable local BLAST manager.
• BLAST queries against multiple local databases.
• Customized interface to search and view BLAST hits graphically.
• Hyperlinked and downloadable accessions to import BLAST hits on a single click.
• Search dbSNP based on user defined parameters.

Sequence Alignments
• New Alignment Editor 
• Align sequence pairs through Global and Local alignments.
• Dot plots for possible alignments, and secondary structures.
• Display alignment results using user-configurable color scheme.
• Align multiple sequences.
• Edit and save the alignments to a local database.
• Save alignments in Fasta, PFAM, MSF, Clustal, BLC, PIR formats and associated trees in newick format.
• Analyze Phylogenetic relationships using neighbor joining algorithm and UPGMA.

Electropherogram Viewer
• Import all major chromatogram formats (e.g. .abi, .scf, .abd)
• Import, export and modify chromatograms.
• Analyze the quality of sequence information.
• Manipulate the chromatogram data for filtering weak signals.

Contig Assembly
• Automatically align and assemble large numbers of sequences into contigs.
• Allows overlap region length selection, fragment inversion check and identification of consensus regions.
• Save contig results and export contig map.

DNA Sequence Analysis
• Retrieve sequences in all standard sequence formats EMBL, Genbank, FASTA, DDBJ and popular sequence analysis software.
• Feature information and annotations are loaded automatically.
• Monitor the quality of imported sequence information.
• Import chromatograms directly from sequencing machines.
• Create and manipulate sequences using Sequence Editor.

Protein Sequence Analysis
• Reverse translation.
• Protease digest.
• Generate plots for Amino acid frequency, amino acid weights, Charge vs pH, and by Hydrophobicity.
• View statistics for various physico-chemical properties of the protein sequence.
• Analyze protein sequence for hydrophobicity, with helical wheel or beta staircase representations.

Pattern Search
• Search for DNA patterns, motifs and domains.
• Search across a sequence or entire experiments.
• Create your own patterns and save them for future.

Restriction Analysis
• Simulate restriction analysis experiment.
• Define custom enzyme sets.
• View cut site and restriction information.
• Graphical view of RE analysis for ease of work and comprehension.

Primer Design
• Degenerate primer design to amplify homologous sequences.
• Design optimal Primers for PCR and sequencing.
• Design primers unique to entire sequence or to a selected region.
• Analyze Primers for dimers and hairpins.
• Export results in spread sheet format.
• Generate PCR products to save as oligos for further analysis.

Cloning Module
• Design new vectors with RE-based cloning supported by graphical interface of sequences.
• Facilitates LR and BP reactions of Gateway cloning protocols.
• Generates B-cassettes through PCR amplification.

Data Management Capabilities
• Relational database support to organize experiment data.
• Store and manage DNA, protein, vector sequences, Restriction Enzymes, Oligonucleotides and BLAST Results.
• Client server architecture to share your data over an internal network.
• Import and export data in all popular formats and share results with your colleagues.
• Define user specific privileges to access data.

Extensive web interface
• Connect to several public database and utilities from the application.
• Add, delete or edit your own set of regularly used URLs.

Local BLAST Manager
• Create and manage databases and their sequences on any Server.
• Apply the powerful BLAST searches against multiple databases using an ordinary desktop or laptop computer.

Technical Support
Ocimum's technical support staff is available 24 hours, five days a week, to answer your questions about Genchek™ over phone, e-mail and web chat.

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