Sequence Analysis Tools for Molecular Biologists

Home MacVectorDown2x Assembler2x Downloads Try HowToBuy Support Contact Forums

Protein Analysis

MacVector provides a wide range of tools for analyzing Protein sequences. In addition to the single sequence analyses present below, you can also align multiple proteins using ClustalW and scan databases for related proteins over the Internet or locally on your own file system.

Protein Analysis Toolbox

MacVector provides a variety of algorithms that you can use to analyze the composition of protein sequences. These range from simple composition reports (counts of each amino acid, pI and molecular weight) to hydrophobicity, antigenicity and secondary structure predictions. All are accessed through a single Protein Profile Analysis dialog.


The available algorithms in the Protein Analysis Toolbox are:

Amino Acid Composition

Molecular Weight


Parker Antigenicity

Protrusion Index Antigenicity

Welling Antigenicity

Antigenic Index

Kyte/Doolittle hydrophilicity

Hopp/Woods hydrophilicity

GES hydrophilicity

Fauchere/Pliska hydrophobicity

Janin hydrophobicity

Manavalan hydrophobicity

Sweet/Eisenberg hydrophobicity

von Heijne hydrophilicity

Argos transmembrane

von Heijne transmembrane

Protein flexibility

Amphiphilic Helix

Amphiphilic Sheet

Surface Probability

Chou Fasman secondary structure

Robson Garnier secondary structure

The results can be viewed graphically using filled plots so that you can see at a glance if a protein is above or below the average for the displayed analysis. As with the DNA coding preference plots, you can zoom in to the residue level to closely examine interesting regions.


The use of filled plots

In addition to the graphical display, the results can be viewed in tab-delimited text format. This output is designed so that you can copy the text and paste it into Microsoft Excel so that you can perform additional statistical analysis or combine plots for graphical display.


You can copy the tab-delimited

Proteolytic Enzyme Searches

MacVector lets you scan a protein sequence for proteolytic enzyme cleavage sites in a similar way to searching DNA sequences for restriction sites. MacVector provides a reference file containing all of the currently known useful proteolytic enzymes and you can add your own using the built-in editor. The results can be viewed in text or graphical format, with similar filtering options to those available for restriction enzyme searches.

Amino Acid Motif Searches

MacVector can search for Amino Acid subsequences using a very similar approach to the Proteolytic Enzyme searching functionality. However, you can use subsequences with complex patterns for the search - each pattern can have up to three distinct segments, separated by variable inter-segment regions, and you can control the overall similarity required for a match as well as defining residues which must be 100% conserved. MacVector ships with a number of default amino acid subsequence files derived from the popular PROSITE database.

Reverse Translation

You can reverse translate a protein into its equivalent degenerate DNA sequence using the translation code of your choosing. In addition to creating the corresponding DNA sequence, MacVector can also scan the sequence for the least degenerate nucleotide sequences than can be used as probes or PCR primers to identify those sequences in a genomic library.

Dot-Plot Analysis

Pairs of protein sequences can be scanned for sequence similarity to each other using the Dot-Plot functionality, in a similar way to DNA sequences. However, you can also compare a protein sequence to a DNA sequence to identify weak relationships between a protein sequence and a related protein-encoding DNA sequence.


A weak relationship between the

Fig.1  The protein profile


Copyright © 2023 MacVector, Inc. All rights reserved. Terms of Use.

MacVector, Inc • PO Box 1147 • Apex • North Carolina 27502 • USA

phone: +1-919-303-7450 • toll free: +1-866-338-0222 • fax: +1-919-303-7449


Comparison of MacVector Editions

MacVector Cloning Edition

What has changed since my version?

What's New in MacVector?

Graphical Sequence Editing

Agarose Gel Simulation

Gateway and TOPO Cloning

Gibson/LIC Assembly


Primer Design

DNA Analysis

Protein Analysis

Database Searching

Multiple Sequence Alignment

Sequence Confirmation

cDNA Alignment

macOS Mojave Dark Mode

System Requirements