Integrated Sequence and Graphical Viewer

• Sequence as single strand, double strand, translation and with annotations
• Publication quality circular and linear sequence maps in 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
• Importing of Multiple BLAST Hit Sequences
• Search dbSNP based on user defined parameters

 

Sequence Alignments

• Sequence 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
• Quality Values display in the Chromatogram Viewer
• Automatic End Clipping based on Quality Values

 

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

 

 

Automatic Vector Trimming

• Performs trimming in one step on multiple sequences
• Allows users to search against any sequence in a specialized non- redundant vector database using BLASTn, trim that region automatically
• Trimmed sequences information shown in graphical viewer with facility to print and export results

 

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

Feature Extraction Tool

• Allows for Feature Extraction on DNA/Vector/Protein sequences with facility to print and export results

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 Secondary Structures
• Facility to export and save Primers for further analysis

 

TaqMan® Probe Design

• Performs TaqMan design with Secondary structure search and Cross Homology
• Probe will be searched for whole sequence length, 5′ biased or 3′ biased, search ranges of interest
• TaqMan Design allows import of Online Sequences and perform TaqMan Design on them
• Allows users to view TaqMan probes for single sequence or view all the found TaqMan for that sequences on result table

Exon Junction Primer Design

• Locates exon positions and number of exons in the sequences
• Primer pairs will be designed in the given amplicon range, either sense primer or antisense primer is designed on the exon junction with a facility to export results

SSR Marker Primer Design

• Facilitates searching SSR markers based on motif length range and their frequency
• Allows to perform SSR primer design on single DNA or vector sequence with a facility to export SSR and primer design results

 

 

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

 

Additional Features

• Renaming Multiple Sequences Simultaneously
• Importing Species Names along with the Sequence
• QTL Mapping

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.