Vector NTI Advance

Category Cross-Omics>Sequence Analysis/Tools

Abstract Vector NTI Advance is an advanced desktop sequence analysis and molecular biology data management system. Product offers a comprehensive set of data analysis and management tools that are integrated into a single analytical environment.

This integration allows you to focus on your research objectives and avoid the distractions of data manipulation and reformatting. Vector NTI Advance consists of five (5) integrated modules plus additional tools.

Products features/capabilities include:

1) Vector NTI Module -- includes the ability to:

• a) Create new DNA/RNA and Protein Molecules, Enzymes, Oligos, Gel Markers, Citations, Basic Local Alignment Search Tool (BLAST) Results, and Analysis Results;
• b) Organize large amounts of data in one local database;
• c) Generate graphical restriction maps of DNA/RNA molecules;
• d) Automate common tasks and incorporate new algorithms using Application Programming Interfaces (APIs) to the Sequence Analysis Framework;
• e) Design and test Gateway clones prior to bench work, and manage cloning projects more effectively;
• f) Generate new recombinant molecules by restriction cloning with molecule construction and design capabilities;
• g) Use VectorLink annotation-specific hyperlinks to the right Invitrogen reagents for cloning experiments;
• h) Run BLAST searches of the NCBI or LabShare databases, view the results graphically, and download the hits with the click of a button;
• i) Have seamless BLAST searching of the Invitrogen Ultimate Open Reading Frames (ORF) clone collection to obtain the most completely characterized, sequence-verified forms of desired clones;
• j) Obtain support for Microsoft Roaming User Profiles, which allows you access to your own data from multiple computers on the network;
• k) Have tools for centrally administered software deployment - customized installation, licensing, and administration of Vector NTI Advance on hundreds of desktops;
• l) Have automatic up-synchronization of data - ensure robust data management and tracking between Vector NTI Advance and LabShare for Vector NTI;
• m) Design and save PCR primers, sequencing primers, and hybridization probes, and order custom primers online;
• n) Create recombinant molecules with Molecule Construction and Design capabilities;
• o) Monitor and manage parent-descendant relationships between molecules through all ancestors and descendants;
• p) Back translate proteins using any one of thousands of published codon usage tables, or create your own codon usage table;
• q) Visualize and manipulate molecules, including annotations, in Molecule Display windows;
• r) Use the Entrez Search tool to find, download, and store DNA and protein molecules and citations locally;
• s) Predict DNA gel electrophoresis results in silico;
• t) View known 3D structures interactively;
• u) Customize Vector NTI by creating connections to numerous Internet analysis tools;
• v) Seamlessly exchange data with all other modules of Vector NTI Advance.

2) AlignX Module -- includes the ability to:

• a) Create Profile Alignments using a selected sequence;
• b) Do guide tree construction, displayed in an exportable graphical representation;
• c) Have use of standard and user-defined substitution matrices;
• d) Have secondary structure consideration;
• e) Obtain multicolored alignment presentation;
• f) Do automatic consensus calculation(s);
• g) Obtain full alignment editing capabilities;
• h) Do a dot matrix comparison of any two sequences;
• i) Do conversion(s) of Genetics Computer Group (GCG) and Microsoft Solutions Framework (*.msf) files.

3) BioAnnotator Module -- includes the ability to:

• a) Map protein motifs using locally stored copies of the Pfam, PROSITE, and Blocks databases;
• b) Characterize proteolytic cleavage patterns using multiple proteases, taking account of protease cleavage efficiency;
• c) Create and configuration custom proteases;
• d) Annotate protein sequences using motif or protease cleavage results;
• e) Plot physicochemical characteristics of protein sequences using over 50 preloaded analysis scales such as amino acid composition, free energy transfer, etc;
• f) Plot physicochemical properties of DNA sequences using 8 preloaded analysis scales, including melting temperature parameters, guanine-cytosine (GC) content, etc;
• g) Create and configure additional physicochemical analysis scales;
• h) Modify, resize, and overlay multiple analysis plots, and export all graphics to other data presentation applications;
• i) View analysis results in the presence of the feature map and sequence for each molecule under study.

4) ContigExpress Module -- includes the ability to:

• a) Do importing and exporting of DNA/RNA sequences from the Vector NTI Local Database;
• b) Have many supported sequence file formats;
• c) Trim and edit sequence runs individually while viewing chromatogram data;
• d) Batch trim multiple sequence runs using user-defined editing parameters;
• e) Rearrange fragment sequences with the reverse complement tool;
• f) Customize settings for the two assembly algorithms that are available;
• g) Export entire assemblies to files or documents;
• h) View all chromatograms of assembled fragments simultaneously.

5) GenomBench Module -- includes the ability to:

• a) View entire chromosomal banding pattern schematics to guide data import from DAS servers UCSC, Ensembl, TIGR, Wormbase, and Eugenes;
• b) Have multiple, integrated viewers to display genomic sequence, cDNA-genomic DNA alignments, annotated features, and genomic sequence description(s);
• c) Position proprietary DNA sequences along genomic backbones using Spidey or SIM4;
• d) Recover additional information for sequence-based annotations, such as mRNAs and Expressed Sequence Tags (ESTs), directly from GenBank, with the click of a button;
• e) Make annotated sequences aligned with the genomic backbone simply by dragging-and-dropping them into the Alignment Pane;
• f) Save copies of reference DNA sequences, along with all existing and user-created track annotations, to local database storage;
• g) Have all Feature Types (e.g., known genes, sequenced mRNAs, Genscan predictions, etc.) color-coded, and linked directly to their cognate genomic DNA sequences for rapid sequence selection;
• h) Let you specify which Feature Types to download from DAS servers and which to display in the Feature Map Pane;
• i) Create new features and edit existing features, with numerous display and editing options to customize your view of the genome.

3-D Molecule Viewer -- includes the ability to:

• a) Search for structures by keyword, molecule name and many other attributes using the Entrez Search tool in the Vector NTI module;
• b) Download and view structures from any angle, so you can “walk around” your molecule is 3D space;
• c) Zoom, rotate, mark and invert structures, and view in stereo if desired;
• d) Adjust the level of detail and color scheme, and render structures in several ways, such as cartoon display, backbone only, ball-and-stick, and space-fill;
• e) Measure atomic distances, bond lengths and torsion angles or calculate solvent accessible surfaces;
• f) Seamlessly transfer structural motif annotation information onto the sequence of the molecule under study.

What’s New features/capabilities in Vector NTI® 11.5 --

1) Workflow support for new DNA cloning and genome-scale assembly tools;

2) Mac Compatibility and Extended OS support;

3) Improved Workflow for Querying TaqMan® Gene Expression Assays Online;

4) Applied Biosystems® 3500 System File Format Support;

5) Primer-Template Alignment Interface; and

6) Serious performance for managing thousand of molecules.

System Requirements

Contact manufacturer.

Manufacturer

• Invitrogen Corporation
• 5791 Van Allen Way
• PO Box 6482
• Carlsbad, California 92008 USA
• Tel: (760) 603-7200
• Fax: (760) 602-6500
• Email: tech_support@invitrogen.com

Manufacturer Web Site Vector NTI Advance

Price Contact manufacturer.

G6G Abstract Number 20075R

G6G Manufacturer Number 101570