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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 ViewerVisualize and interactively explore biological sequences

Functions

aacountCount amino acids in sequence
codonbiasCalculate codon frequency for each amino acid coded for in nucleotide sequence
codoncountCount codons in nucleotide sequence
nmercountCount n-mers in nucleotide or amino acid sequence
seqwordcountCount number of occurrences of word in sequence
aa2ntConvert amino acid sequence to nucleotide sequence
nt2aaConvert nucleotide sequence to amino acid sequence
aa2intConvert amino acid sequence from letter to integer representation
int2aaConvert amino acid sequence from integer to letter representation
revgeneticcodeReturn reverse mapping (amino acid to nucleotide codon) for genetic code
aminolookupFind amino acid codes, integers, abbreviations, names, and codons
geneticcodeReturn nucleotide codon to amino acid mapping for genetic code
atomiccompCalculate atomic composition of protein
isoelectricEstimate isoelectric point for amino acid sequence
isotopicdistCalculate high-resolution isotope mass distribution and density function
molweightCalculate molecular weight of amino acid sequence
seqviewerVisualize and interactively explore biological sequences
seqdispFormat long sequence output for easy viewing
seqshoworfsDisplay open reading frames in sequence
seqshowwordsGraphically display words in sequence
proteinplotOpen Protein Plot window to investigate properties of amino acid sequence
proteinpropplotPlot properties of amino acid sequence
ramachandranDraw Ramachandran plot for Protein Data Bank (PDB) data
seqconsensusCalculate consensus sequence
seqdotplotCreate dot plot of two sequences
seqlogoDisplay sequence logo for nucleotide or amino acid sequences
seqprofileCalculate sequence profile from set of multiply aligned sequences
seqinsertgapsInsert gaps into nucleotide or amino acid sequence
cleaveCleave amino acid sequence with enzyme
cleavelookupFind cleavage rule for enzyme or compound
seq2regexpConvert sequence with ambiguous characters to regular expression
featuresparseParse features from GenBank, GenPept, or EMBL data
featureparseParse features from GenBank, GenPept, or EMBL data
randseqGenerate random sequence from finite alphabet
seqmatchFind 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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