Nucleotide Sequence Analysis

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

Apps

Sequence ViewerVisualize and interactively explore biological sequences

Functions

basecountCount nucleotides in sequence
codonbiasCalculate codon frequency for each amino acid coded for in nucleotide sequence
codoncountCount codons in nucleotide sequence
dimercountCount dimers in nucleotide sequence
ntdensityPlot density of nucleotides along sequence
seqwordcountCount number of occurrences of word in sequence
nt2aaConvert nucleotide sequence to amino acid sequence
aa2ntConvert amino acid sequence to nucleotide sequence
nt2intConvert nucleotide sequence from letter to integer representation
int2ntConvert nucleotide sequence from integer to letter representation
dna2rnaConvert DNA sequence to RNA sequence
rna2dnaConvert RNA sequence to DNA sequence
revgeneticcodeReturn reverse mapping (amino acid to nucleotide codon) for genetic code
seqcomplementCalculate complementary strand of nucleotide sequence
seqrcomplementCalculate reverse complementary strand of nucleotide sequence
seqreverseCalculate reverse strand of nucleotide sequence
baselookupFind nucleotide codes, integers, names, and complements
geneticcodeReturn nucleotide codon to amino acid mapping for genetic code
oligopropCalculate sequence properties of DNA oligonucleotide
cpgislandLocate CpG islands in DNA sequence
joinseqJoin two sequences to produce shortest supersequence
palindromesFind palindromes in sequence
randseqGenerate random sequence from finite alphabet
seqmatchFind matches for every character vector in library
seqviewerVisualize and interactively explore biological sequences
seqdispFormat long sequence output for easy viewing
seqshoworfsDisplay open reading frames in sequence
featureparseParse features from GenBank, GenPept, or EMBL data
featureviewDraw linear or circular map of features from GenBank structure
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
rebasecutsFind restriction enzymes that cut nucleotide sequence
restrictSplit nucleotide sequence at restriction site
seq2regexpConvert sequence with ambiguous characters to regular expression

Topics

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.

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

Analyzing Synonymous and Nonsynonymous Substitution Rates

Analyzing Synonymous and Nonsynonymous Substitution Rates

How the analysis of synonymous and nonsynonymous mutations at the nucleotide level can suggest patterns of molecular adaptation in the genome of HIV-1. This example is based on the discussion of natural selection at the molecular level presented in Chapter 6 of "Introduction to Computational Genomics. A Case Studies Approach" [1].

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Exploring Primer Design

Exploring Primer Design

Use the Bioinformatics Toolbox™ to find potential primers that can be used for automated DNA sequencing.

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Identifying Over-Represented Regulatory Motifs

Identifying Over-Represented Regulatory Motifs

Illustrates a simple approach to searching for potential regulatory motifs in a set of co-expressed genomic sequences by identifying significantly over-represented ungapped words of fixed length. The discussion is based on the case study presented in Chapter 10 of "Introduction to Computational Genomics. A Case Studies Approach" [1].

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Bioinformatics Toolbox Documentation

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