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Nucleotide Sequence Analysis

Calculate and interactively explore sequence statistics; calculate sequence properties; analyze motifs; design primers; find restriction enzymes

Apps

Sequence Viewer Visualize and interactively explore biological sequences

Functions

basecount Count nucleotides in sequence
codonbias Calculate codon frequency for each amino acid coded for in nucleotide sequence
codoncount Count codons in nucleotide sequence
dimercount Count dimers in nucleotide sequence
ntdensity Plot density of nucleotides along sequence
seqwordcount Count number of occurrences of word in sequence
nt2aa Convert nucleotide sequence to amino acid sequence
aa2nt Convert amino acid sequence to nucleotide sequence
nt2int Convert nucleotide sequence from letter to integer representation
int2nt Convert nucleotide sequence from integer to letter representation
dna2rna Convert DNA sequence to RNA sequence
rna2dna Convert RNA sequence to DNA sequence
revgeneticcode Return reverse mapping (amino acid to nucleotide codon) for genetic code
seqcomplement Calculate complementary strand of nucleotide sequence
seqrcomplement Calculate reverse complementary strand of nucleotide sequence
seqreverse Calculate reverse strand of nucleotide sequence
baselookup Find nucleotide codes, integers, names, and complements
geneticcode Return nucleotide codon to amino acid mapping for genetic code
oligoprop Calculate sequence properties of DNA oligonucleotide
cpgisland Locate CpG islands in DNA sequence
joinseq Join two sequences to produce shortest supersequence
palindromes Find palindromes in sequence
randseq Generate random sequence from finite alphabet
seqmatch Find matches for every character vector in library
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
featuresmap Draw linear or circular map of features from GenBank structure
featureparse Parse features from GenBank, GenPept, or EMBL data
featuresparse Parse features from GenBank, GenPept, or EMBL data
featureview Draw linear or circular map of features from GenBank structure
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
rebasecuts Find restriction enzymes that cut nucleotide sequence
restrict Split nucleotide sequence at restriction site
seq2regexp Convert sequence with ambiguous characters to regular expression

Examples and How To

Exploring a Nucleotide Sequence Using Command Line

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

Exploring a Nucleotide Sequence Using the Sequence Viewer App

Use a graphical interface for the sequence functions.

Concepts

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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