Category Cross-Omics>Sequence Analysis/Tools and Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions.

MacVector Major features/capabilities --

1) Graphical Sequence Editing -- MacVector can read and write DNA and Protein sequences in most popular file formats. In addition to directly editing sequences and features/annotations, MacVector has an intuitive “Click Cloning” graphical interface that lets you easily replicate laboratory cloning experiments to create new molecules.

MacVector uses the native Mac OS X Quartz graphics to generate publication quality images that can be scaled to any size with No loss of resolution.

Sequences can be edited using the fully functional Sequence Editor. As well as ensuring that feature locations are correctly maintained during edits, an audio function lets you playback selected residues for easy proofreading. Toolbar buttons let you view and edit the features, annotations, and graphics associated with each sequence.

The sequence editor also acts as the primary window from which you can launch all MacVector analyses. All functions are integrated into a single MacVector application - No need to switch to a different module or program to find the algorithm you are looking for.

2) Gateway and Topo Cloning -- MacVector supports the popular Gateway, TOPO TA and Zero Blunt cloning technologies from Invitrogen. With a few simple clicks from an intuitive graphical interface, you can replicate your ‘biological manipulations’ at the bench to create new molecules with the correct sequences across the cloning and recombination junctions.

3) Auto Annotation -- You can scan an unannotated or partially annotated sequence against a folder on your hard drive and MacVector will identify matching features in sequences in the target folder and add them to your sequence. Because MacVector includes ‘custom feature’ appearance information when annotating the sequence, you can use this to maintain a carefully curated set of your favorite genes and sequences each with a ‘graphical appearance’ that best suits your needs.

4) Primer Design -- You can design primers for either PCR or Sequencing/Hybridization probes using the primer design functions. In addition, you can test specific primers to determine if they have secondary structure problems, alternate binding sites or other characteristics that might impact their use in experiments.

5) DNA Analysis -- MacVector provides a wide variety of useful DNA analysis tools, including base composition analysis, Restriction Enzyme searches, DNA Subsequence searches and “Dot-Plot” comparisons between DNA:DNA and DNA:Protein sequences. A Coding Preference toolbox lets you select a variety of algorithms to graphically scan a DNA sequence for likely protein coding open reading frames.

6) Protein Analysis -- Protein sequences can be reverse translated into DNA, compared using “Dot-Plot” analysis, and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive ‘Protein Analysis Toolbox’ provides a wide variety of algorithms for analyzing the composition of proteins and presenting the results in graphical and tabular formats.

7) Database Searching -- MacVector has built-in Internet connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc. and directly download them into MacVector, complete with all features and annotations.

The built-in BLAST interface lets you submit multiple BLAST jobs using DNA or Protein sequences and then download any matching sequences by selecting them from a hit list.

Even without an Internet connection, MacVector can align sequences against any folder on your hard drive using a FastA algorithm, allowing for “local” database searches.

8) Multiple Sequence Alignment -- You can align unlimited numbers of DNA or Protein sequences using the ClustalW algorithm built in to MacVector. A full-featured editor lets you make manual adjustments to the alignments and view them using a wide variety of customizable color schemes.

You can create publication quality graphical outputs of the alignments and view pairwise combinations of the sequences in aligned and matrix formats.

9) Sequence Assembly -- Sequence Assembly functionality in MacVector is now provided by two (2) modules. First there is a built-in function called ‘Align To Reference’. This can be used for two (2) different functions, ‘Sequence Confirmation’ and ‘cDNA Alignment’.

This is included with MacVector and allows you to import ‘trace files’ or ‘sequence files’ and assemble them against a template sequence. This is ideal for small scale sequencing projects, especially resequencing.

For example, checking an in situ mutagenesis experiment, a construct you've just made, or confirming the sequence of a cloned PCR fragment. It's also an excellent tool for SNP analysis, with some special tools to allow you to easily spot mutations from your original template sequence.

For full scale sequencing projects where you do Not know the sequence you'll need MacVector and a separately purchased plug-in called Assembler (see below...).

This is a full contig assembly application that uses the Phred, Phrap and cross-match algorithms from the University of Washington to assemble traces into contigs.

It displays full quality scores of the reads and the aligned contigs. The trial version of MacVector also includes the Assembler plug-in.

10) MacVector Assembler -- Assembler is a MacVector add-on software module for assembling DNA sequence reads into contig assemblies.

Based on the industry standard algorithms of Phred and Phrap, Assembler is Not only an excellent tool for your small genome projects, sequence comparisons, and SNP studies, but it also provides you with high performance and high quality ‘sequence assembly’.

Assembler Key Scientific Functionality -

a) Base Calling - Carry out highly accurate base calling from chromatograms, and generate useful quality values for each individual base call using Phred. An interactive ‘trace editor’ allows you to view the base calls and their quality values.

b) Sequence Assembly - Perform ultra fast sequence assembly using Phrap to generate a consensus sequence. (1,000 sequences can be assembled in a few minutes). You can adjust numerous Phrap parameters such as mismatch penalty, gap penalty, etc. to optimize your assembly.

c) Trim and Mask Vector Sequences - Eliminate vector contamination sequences using cross-match. You can easily designate and select your own vector sequence files.

d) Contig Editing and Analysis - Edit individual bases in a DNA sequence to generate a new consensus. View the consensus sequence, all associated chromatograms, sequence reads, and quality scores in the intuitive easy-to-use, ‘graphical contig editor’.

When variations in DNA sequences are observed, you can quickly identify alternative ‘protein sequences’ by performing an open reading frame analysis. Alternatively see a real-time 3/6 frame translation of your contigs in the integrated contig editor.

e) Next Generation Sequencing - The optional add-on Assembler module has been enhanced to provide support for ‘next generation sequencing’ machines. Short read data may be imported in Fastq format and assembled using the latest version of Phrap. Illumina, 454 and Solid data all supported in Fastq format.

f) Supports Numerous File Formats - Effortlessly import ABI, SCF, and ALF formatted chromatogram files, MacVector, Fastq or FASTA formatted sequence files.

g) Easy to use interface - Navigating around your assemblies has never been easier. Display an entire contig in the graphical Map view, and select a read to zoom straight to show that section in the Editor view at sequence level. Click on a base in the alignment and see the trace data associated with that base below.

h) Job Manager - Assembler uses the MacVector ‘job manager’ to control base calling and assembly. This allows you to continue working while running longer assemblies.

System Requirements

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Manufacturer Web Site MacVector

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G6G Abstract Number 20548

G6G Manufacturer Number 104163