Protein and Amino Acid Sequence Analysis

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

Apps

Sequence Viewer

Visualize and interactively explore biological sequences

Functions

`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

`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

`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

`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`	Draw Ramachandran plot for Protein Data Bank (PDB) data

`seqconsensus`	Calculate consensus sequence
`seqdotplot`	Create dot plot of two sequences
`seqlogo`	Display sequence logo for nucleotide or amino acid sequences
`seqprofile`	Calculate sequence profile from set of multiply aligned sequences
`seqinsertgaps`	Insert gaps into nucleotide or amino acid sequence

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

`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

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™.

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