Category Cross-Omics>Sequence Analysis/Tools

Abstract Genchek is a comprehensive, multi-platform, sequence analysis software package. It facilitates the analysis of Expressed Sequence Tags (ESTs), Complete Genome, and Single Nucleotide Polymorphism (SNP) 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 contains 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.

Genchek features/capabilities include:

Integrated Sequence and Graphical Viewer includes --

1) Sequence as a single strand, double strand, translation and with annotations;

2) Publication quality circular and linear sequence maps via the manufacturer’s graphical viewer;

3) A graphical view of restriction maps that facilitates easy cloning;

4) A graphical view of Open Reading Frames (ORFs) in the sequence maps; and

5) Imported and user defined sequence annotations in graphical and sequence views.

Basic Local Alignment Search Tool (BLAST) Suite includes --

1) Support for blastn, blastp, blastx, tblastn, tblastx, and Batch Blast;

2) The ability to create customized local BLAST databases through the manufacturer’s pluggable local BLAST manager;

3) BLAST queries against multiple local databases;

4) A customized interface to search and view BLAST hits graphically;

5) Hyperlinked and downloadable accessions to import BLAST hits on a single click; and

6) The ability to search the Single Nucleotide Polymorphism database (dbSNP) based on user defined parameters.

Sequence Alignments includes --

1) A Sequence Alignment Editor;

2) Align sequence pairs through Global and Local alignments;

3) Dot plots for possible alignments, and secondary structures;

4) The ability to display alignment results using a user-configurable color scheme;

5) The ability to align multiple sequences;

6) The ability to edit and save the alignments to a local database;

7) The ability to save alignments in Fasta, PFAM, MSF, CLUSTAL, BLC, PIR formats and associated trees in the Newick format; and

8) The ability to analyze Phylogenetic relationships using the neighbor joining algorithm and the Unweighted Pair Group Method with Arithmetic mean (UPGMA).

Electropherogram Viewer includes the ability to --

1) Import all major chromatogram formats (e.g. Applied Biosystems (.abi), standard chromatogram format (.scf), .abd);

2) Import, export and modify chromatograms;

3) Analyze the quality of sequence information;

4) Manipulate the chromatogram data for the filtering of weak signals;

5) Provide Quality Values display in the Chromatogram Viewer; and

6) Provide Automatic End Clipping based on Quality Values.

Contig (a set of overlapping DNA segments derived from a single genetic source) Assembly includes the ability to --

1) Automatically align and assemble large numbers of sequences into contigs;

2) Allow overlap region length selection, fragment inversion check and the identification of consensus regions; and

3) Save contig results and export a contig map.

Automatic Vector Trimming --

1) Performs trimming in one step on multiple sequences;

2) Allows users to search against any sequence in a specialized non-redundant vector database using BLASTn, and trim that region automatically; and

3) Trimmed sequences information can be displayed in the graphical viewer with the facility to print and export results.

DNA Sequence Analysis includes the ability to --

1) Retrieve sequences in all standard sequence formats EMBL, GenBank, FASTA, DDBJ and popular sequence analysis software;

2) Have feature information and annotations loaded automatically;

3) Monitor the quality of imported sequence information;

4) Import chromatograms directly from sequencing machines; and

5) Create and manipulate sequences using the Sequence Editor.

Feature Extraction Tool --

1) Allows for Feature Extraction on DNA/Vector/Protein sequences with the facility to print and export results.

Protein Sequence Analysis includes the ability to --

1) Do reverse translation;

2) Do Protease digest;

3) Generate plots for Amino acid frequency, amino acid weights, Charge vs. pH, and by Hydrophobicity;

4) View statistics for various physico-chemical properties of the protein sequence; and

5) Analyze protein sequence for hydrophobicity, with helical wheel or beta staircase representations.

Pattern Search includes the ability to --

1) Search for DNA patterns, motifs, and domains;

2) Search across a sequence or entire experiments; and

3) Create your own patterns and save them for future usage.

Restriction Analysis includes the ability to --

1) Simulate a restriction analysis experiment;

2) Define custom enzyme sets;

3) View a cut site and restriction information; and

4) Give you a graphical view of Restriction Endonuclease (RE) analysis for increased comprehension.

Primer Design includes the ability to -

1) Degenerate primer design to amplify homologous sequences;

2) Design optimal Primers for Polymerase Chain Reaction (PCR) and sequencing;

3) Design primers unique to the entire sequence or to a selected region;

4) Analyze Primers for Secondary Structures; and

5) Export and save Primers for further analysis.

TaqMan® Probe Design --

1) Performs TaqMan design with Secondary structure search and Cross Homology;

2) Probe can be searched for whole sequence length, 5' biased or 3' biased, and search ranges of interest;

3) TaqMan Design allows the import of Online Sequences and it can perform TaqMan Design on them; and

4) Allows users to view TaqMan probes for a single sequence or to view all found TaqMan for that sequence, on a result table.

Exon Junction Primer Design --

1) Can locate exon positions and the number of exons in sequences; and

2) Primer pairs can be designed in a given amplicon range, either the sense primer or antisense primer can be designed on the exon junction, with a facility to export results.

SSR Marker Primer Design --

1) Facilitates searching SSR markers based on the motif length range and their frequency; and

2) Allows you to perform SSR primer design on a single DNA or vector sequence, with a facility to export SSR and primer design results.

Cloning Module --

1) Can be used to design new vectors with RE-based cloning supported by the graphical interface of sequences;

2) Facilitates LR and BP reactions of Gateway cloning protocols; and

3) Can generate B-cassettes through PCR amplification.

Data Management Capabilities include the ability to --

1) Have relational database support to organize your experiment data;

2) Store and manage DNA, protein, vector sequences, Restriction Enzymes, Oligonucleotides and BLAST Results;

3) Have a client server architecture to share your data over an internal network;

4) Import and export data in all popular formats and share results with your colleagues; and

5) Define user specific privileges to access data.

Extensive Web interface includes the ability to --

1) Connect to several public database and utilities from your application; and

2) Add, delete or edit your own set of regularly used Uniform Resource Locators (URLs).

Local BLAST Manager includes the ability to --

1) Create and manage databases and their sequences on any Server;

2) Apply advanced BLAST searches against multiple databases using an ordinary desktop or laptop computer.

Additional Features --

1) Renaming Multiple Sequences Simultaneously;

2) Importing Species Names along with the Sequence; and

3) QTL Mapping.

Note: See G6G Abstract Number 20074R for additional product info from this manufacturer.

System Requirements

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Manufacturer Web Site Genchek

Price Contact manufacturer.

G6G Abstract Number 20073R

G6G Manufacturer Number 102025