Protein and Amino Acid Sequence Analysis

Calculate and interactively explore amino acid sequence statistics; calculate sequence properties; find cleavage enzymes

Perform in-depth analyses of amino acid sequences to get better understanding of sequence features and functions. You can compute sequence statistics, such as codon frequency and atomic composition of a protein, and interactively explore the sequences in the Sequence Viewer app. Calculate molecular weight and estimate isoelectric points of amino acid sequences. Use various utility and plotting functions to display open reading frames, draw Ramachandran plot for PDB data, and display properties, such as hydrophobicity of residues, of amino acid sequences.

Apps

Sequence Viewer

Visualize and interactively explore biological sequences

Functions

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Compute Sequence Statistics

`aacount`	Count amino acids in sequence
`codonbias`	Calculate codon frequency for each amino acid coded for in nucleotide sequence
`codoncount`	Count codons in nucleotide sequence
`nmercount`	Count n-mers in nucleotide or amino acid sequence
`seqwordcount`	Count number of occurrences of word in sequence

Convert Sequences

`aa2nt`	Convert amino acid sequence to nucleotide sequence
`nt2aa`	Convert nucleotide sequence to amino acid sequence
`aa2int`	Convert amino acid sequence from letter to integer representation
`int2aa`	Convert amino acid sequence from integer to letter representation
`revgeneticcode`	Return reverse mapping (amino acid to nucleotide codon) for genetic code
`aminolookup`	Find amino acid codes, integers, abbreviations, names, and codons
`geneticcode`	Return nucleotide codon to amino acid mapping for genetic code

Analyze Sequence Features

`atomiccomp`	Calculate atomic composition of protein
`isoelectric`	Estimate isoelectric point for amino acid sequence
`isotopicdist`	Calculate high-resolution isotope mass distribution and density function
`molweight`	Calculate molecular weight of amino acid sequence
`seqconsensus`	Calculate consensus sequence
`seqprofile`	Calculate sequence profile from set of multiply aligned sequences
`seqinsertgaps`	Insert gaps into nucleotide or amino acid sequence
`featureparse`	Parse features from GenBank, GenPept, or EMBL data
`randseq`	Generate random sequence from finite alphabet
`seqmatch`	Find matches for every character vector in library

Visualize Sequences

`seqviewer`	Visualize and interactively explore biological sequences
`seqdisp`	Format long sequence output for easy viewing
`seqshoworfs`	Display open reading frames in sequence
`proteinplot`	Open Protein Plot window to investigate properties of amino acid sequence
`proteinpropplot`	Plot properties of amino acid sequence
`ramachandran`	Ramachandran plot for Protein Data Bank (PDB) data
`seqdotplot`	Create dot plot of two sequences
`seqlogo`	Display sequence logo for nucleotide or amino acid sequences

Cleave Sequences

`cleave`	Cleave amino acid sequence with enzyme
`cleavelookup`	Find cleavage rule for enzyme or compound
`seq2regexp`	Convert sequence with ambiguous characters to regular expression

Topics

Explore a Protein Sequence Using the Sequence Viewer App
Use the Biological Sequence Viewer to investigate protein sequences.
Compare Sequences Using Sequence Alignment Algorithms
Determining the similarity between two sequences is a common task in computational biology.
Protein Property Analysis
You can use a collection of protein analysis methods to extract information from your data.
Sequence Utilities and Statistics
You can manipulate and analyze your sequences to gain a deeper understanding of the physical, chemical, and biological characteristics of your data.

Featured Examples

Investigating the Bird Flu Virus

Calculate Ka/Ks ratios for eight genes in the H5N1 and H2N3 virus genomes, and perform a phylogenetic analysis on the HA gene from H5N1 virus isolated from chickens across Africa and Asia. For the phylogenetic analysis, you will reconstruct a neighbor-joining tree and create a 3-D plot of sequence distances using multidimensional scaling. Finally, you will map the geographic locations where each HA sequence was found on a regional map. Sequences used in this example were selected from the bird flu case study on the Computational Genomics Website [1]. Note: The final section in this example requires the Mapping Toolbox™.

Open Script

Calling Bioperl Functions from MATLAB

The interoperability between MATLAB® and Bioperl - passing arguments from MATLAB to Perl scripts and pulling BLAST search data back to MATLAB.

Open Script