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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
seqshowwords Graphically display words 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
featuresparse Parse features from GenBank, GenPept, or EMBL data
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

Examples and How To

Exploring a Nucleotide Sequence Using Command Line

Starting with a DNA sequence, calculate statistics for the nucleotide content.

Explore a Protein Sequence Using the Sequence Viewer App

Use the Biological Sequence Viewer to investigate protein sequences

Compare Sequences Using Sequence Alignment Algorithms

Starting with a DNA sequence for a human gene, locate and verify a corresponding gene in a model organism.

Concepts

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.

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