Bioinformatics Toolbox™

Function Reference

Constructor	Create objects.
Data Formats and Databases	Read data into the MATLAB^® software from Web databases; read and write to files using specific sequence data formats.
Trace Tools	Read data from SCF file and draw nucleotide trace plots.
Sequence Conversion	Convert nucleotide and amino acid sequences between character and integer formats, reverse and complement order of nucleotide bases, and translate nucleotides codons to amino acids.
Sequence Utilities	Calculate consensus sequence from set of multiply aligned sequences, run BLAST search from MATLAB^® environment, and search sequences using regular expressions.
Sequence Statistics	Determine base counts, nucleotide density, codon bias, and CpG islands; search for words and identify open reading frames (ORFs).
Sequence Visualization	Visualize sequence data.
Pairwise Sequence Alignment	Compare nucleotide or amino acid sequences using pairwise sequence alignment functions.
Multiple Sequence Alignment	Compare sets of nucleotide or amino acid sequences; progressively align sequences using phylogenetic tree for guidance.
Scoring Matrices	Standard scoring matrices such as PAM and BLOSUM families of matrices that alignment functions use.
Phylogenetic Tree Tools	Read phylogenetic tree files, calculate pairwise distances between sequences, and build a phylogenetic tree.
Graph Theory	Apply basic graph theory algorithms to sparse matrices.
Gene Ontology	Read Gene Ontology formatted files.
Protein Analysis	Determine protein characteristics and simulate enzyme cleavage reactions.
Profile Hidden Markov Models	Get profile hidden Markov model data from the PFAM database or create your own profiles from set of sequences.
Microarray File Formats	Read data from common microarray file formats including Affymetrix^® GeneChip^®, ImaGene^® results, and SPOT files; read GenePix^® GPR and GAL files.
Microarray Utility	Using Affymetrix^® and GeneChip^® data sets, get library information for probe, gene information from probe set, and probe set values from CEL and CDF information; show probe set information from the NetAffx™ Web site and plot probe set values.
Microarray Data Analysis and Visualization	Analyze and visualize microarray data with t tests, spatial plots, box plots, loglog plots, and intensity-ratio plots.
Microarray Normalization and Filtering	Normalize microarray data with lowess and mean normalization functions; filter raw data for cleanup before analysis.
Statistical Learning	Classify and identify features in data sets, set up cross-validation experiments, and compare different classification methods.
Mass Spectrometry File Formats, Preprocessing, and Visualization	Read data from common mass spectrometry file formats, preprocess raw mass spectrometry data from instruments, and analyze spectra to identify patterns and compounds.

Constructor

biograph	Create `biograph object`
clustergram	Compute hierarchical clustering, display dendrogram and heat map, and create `clustergram object`
geneont	Create `geneont object`
phytree	Create `phytree object`

Data Formats and Databases

affyprobeseqread	Read data file containing probe sequence information for Affymetrix^® GeneChip^® array
affyread	Read microarray data from Affymetrix^® GeneChip^® file
agferead	Read Agilent^® Feature Extraction Software file
blastformat	Create local BLAST database
blastread	Read data from NCBI BLAST report file
blastreadlocal	Read data from local BLAST report
celintensityread	Read probe intensities from Affymetrix^® CEL files
cytobandread	Read cytogenetic banding information
emblread	Read data from EMBL file
fastaread	Read data from FASTA file
fastawrite	Write to file using FASTA format
galread	Read microarray data from GenePix^® array list file
genbankread	Read data from GenBank^® file
genpeptread	Read data from GenPept file
geosoftread	Read Gene Expression Omnibus (GEO) SOFT format data
getblast	Retrieve BLAST report from NCBI Web site
getembl	Retrieve sequence information from EMBL database
getgenbank	Retrieve sequence information from GenBank^® database
getgenpept	Retrieve sequence information from GenPept database
getgeodata	Retrieve Gene Expression Omnibus (GEO) SOFT format data
gethmmalignment	Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
gethmmprof	Retrieve hidden Markov model (HMM) profile from PFAM database
gethmmtree	Retrieve phylogenetic tree data from PFAM database
getpdb	Retrieve protein structure data from Protein Data Bank (PDB) database
gprread	Read microarray data from GenePix^® Results (GPR) file
ilmnbsread	Read gene expression data exported from Illumina^® BeadStudio™ software
imageneread	Read microarray data from ImaGene^® Results file
jcampread	Read JCAMP-DX-formatted files
multialignread	Read multiple-sequence alignment file
mzxmlread	Read data from mzXML file
pdbread	Read data from Protein Data Bank (PDB) file
pdbwrite	Write to file using Protein Data Bank (PDB) format
pfamhmmread	Read data from PFAM HMM-formatted file
phytreeread	Read phylogenetic tree file
phytreewrite	Write phylogenetic tree object to Newick-formatted file
scfread	Read trace data from SCF file
sptread	Read data from SPOT file

Trace Tools

scfread	Read trace data from SCF file
traceplot	Draw nucleotide trace plots

Sequence Conversion

aa2int	Convert amino acid sequence from letter to integer representation
aa2nt	Convert amino acid sequence to nucleotide sequence
aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
baselookup	Find nucleotide codes, integers, names, and complements
dna2rna	Convert DNA sequence to RNA sequence
int2aa	Convert amino acid sequence from integer to letter representation
int2nt	Convert nucleotide sequence from integer to letter representation
nt2aa	Convert nucleotide sequence to amino acid sequence
nt2int	Convert nucleotide sequence from letter to integer representation
rna2dna	Convert RNA sequence of nucleotides to DNA sequence
rnaconvert	Convert secondary structure of RNA sequence between bracket and matrix notations
seq2regexp	Convert sequence with ambiguous characters to regular expression
seqcomplement	Calculate complementary strand of nucleotide sequence
seqrcomplement	Calculate reverse complement of nucleotide sequence
seqreverse	Reverse letters or numbers in nucleotide sequence

Sequence Utilities

aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
baselookup	Find nucleotide codes, integers, names, and complements
blastlocal	Perform search on local BLAST database to create BLAST report
blastncbi	Create remote NCBI BLAST report request ID or link to NCBI BLAST report
cleave	Cleave amino acid sequence with enzyme
featuresparse	Parse features from GenBank^®, GenPept, or EMBL data
geneticcode	Return nucleotide codon to amino acid mapping for genetic code
joinseq	Join two sequences to produce shortest supersequence
oligoprop	Calculate sequence properties of DNA oligonucleotide
palindromes	Find palindromes in sequence
pdbdistplot	Visualize intermolecular distances in Protein Data Bank (PDB) file
proteinplot	Characteristics for amino acid sequences
proteinpropplot	Plot properties of amino acid sequence
ramachandran	Draw Ramachandran plot for Protein Data Bank (PDB) data
randseq	Generate random sequence from finite alphabet
rebasecuts	Find restriction enzymes that cut nucleotide sequence
restrict	Split nucleotide sequence at restriction site
revgeneticcode	Return reverse mapping (amino acid to nucleotide codon) for genetic code
rnafold	Predict minimum free-energy secondary structure of RNA sequence
seqconsensus	Calculate consensus sequence
seqdisp	Format long sequence output for easy viewing
seqinsertgaps	Insert gaps into nucleotide or amino acid sequence
seqlogo	Display sequence logo for nucleotide or amino acid sequences
seqmatch	Find matches for every string in library
seqprofile	Calculate sequence profile from set of multiply aligned sequences
seqshoworfs	Display open reading frames in sequence

Sequence Statistics

aacount	Count amino acids in sequence
aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
basecount	Count nucleotides in sequence
baselookup	Find nucleotide codes, integers, names, and complements
codonbias	Calculate codon frequency for each amino acid coded for in nucleotide sequence
codoncount	Count codons in nucleotide sequence
cpgisland	Locate CpG islands in DNA sequence
dimercount	Count dimers in nucleotide sequence
isoelectric	Estimate isoelectric point for amino acid sequence
molweight	Calculate molecular weight of amino acid sequence
nmercount	Count n-mers in nucleotide or amino acid sequence
ntdensity	Plot density of nucleotides along sequence
seqshowwords	Graphically display words in sequence
seqwordcount	Count number of occurrences of word in sequence

Sequence Visualization

featuresmap	Draw linear or circular map of features from GenBank^® structure
rnaplot	Draw secondary structure of RNA sequence
seqtool	Open tool to interactively explore biological sequences

Pairwise Sequence Alignment

fastaread	Read data from FASTA file
nwalign	Globally align two sequences using Needleman-Wunsch algorithm
seqdotplot	Create dot plot of two sequences
showalignment	Display color-coded sequence alignment
swalign	Locally align two sequences using Smith-Waterman algorithm

Multiple Sequence Alignment

fastaread	Read data from FASTA file
multialign	Align multiple sequences using progressive method
multialignread	Read multiple-sequence alignment file
multialignviewer	Open viewer for multiple sequence alignments
profalign	Align two profiles using Needleman-Wunsch global alignment
seqpdist	Calculate pairwise distance between sequences
showalignment	Display color-coded sequence alignment

Scoring Matrices

blosum	Return BLOSUM scoring matrix
dayhoff	Return Dayhoff scoring matrix
gonnet	Return Gonnet scoring matrix
nuc44	Return NUC44 scoring matrix for nucleotide sequences
pam	Return PAM scoring matrix

Phylogenetic Tree Tools

dnds	Estimate synonymous and nonsynonymous substitution rates
dndsml	Estimate synonymous and nonsynonymous substitution rates using maximum likelihood method
gethmmtree	Retrieve phylogenetic tree data from PFAM database
phytreeread	Read phylogenetic tree file
phytreetool	View, edit, and explore phylogenetic tree data
phytreewrite	Write phylogenetic tree object to Newick-formatted file
seqinsertgaps	Insert gaps into nucleotide or amino acid sequence
seqlinkage	Construct phylogenetic tree from pairwise distances
seqneighjoin	Neighbor-joining method for phylogenetic tree reconstruction
seqpdist	Calculate pairwise distance between sequences

Graph Theory

graphallshortestpaths	Find all shortest paths in graph
graphcluster	Find strongly or weakly connected components in graph
graphconncomp	Find strongly or weakly connected components in graph
graphisdag	Test for cycles in directed graph
graphisomorphism	Find isomorphism between two graphs
graphisspantree	Determine if tree is spanning tree
graphmaxflow	Calculate maximum flow in directed graph
graphminspantree	Find minimal spanning tree in graph
graphpred2path	Convert predecessor indices to paths
graphshortestpath	Solve shortest path problem in graph
graphtopoorder	Perform topological sort of directed acyclic graph
graphtraverse	Traverse graph by following adjacent nodes

Gene Ontology

goannotread	Annotations from Gene Ontology annotated file
num2goid	Convert numbers to Gene Ontology IDs

Protein Analysis

aacount	Count amino acids in sequence
aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
atomiccomp	Calculate atomic composition of protein
cleave	Cleave amino acid sequence with enzyme
evalrasmolscript	Send RasMol script commands to Molecule Viewer window
isoelectric	Estimate isoelectric point for amino acid sequence
molviewer	Display and manipulate 3-D molecule structure
molweight	Calculate molecular weight of amino acid sequence
pdbdistplot	Visualize intermolecular distances in Protein Data Bank (PDB) file
proteinplot	Characteristics for amino acid sequences
proteinpropplot	Plot properties of amino acid sequence
ramachandran	Draw Ramachandran plot for Protein Data Bank (PDB) data

Profile Hidden Markov Models

gethmmalignment	Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
gethmmprof	Retrieve hidden Markov model (HMM) profile from PFAM database
gethmmtree	Retrieve phylogenetic tree data from PFAM database
hmmprofalign	Align query sequence to profile using hidden Markov model alignment
hmmprofestimate	Estimate profile hidden Markov model (HMM) parameters using pseudocounts
hmmprofgenerate	Generate random sequence drawn from profile hidden Markov model (HMM)
hmmprofmerge	Concatenate prealigned strings of several sequences to profile hidden Markov model (HMM)
hmmprofstruct	Create or edit hidden Markov model (HMM) profile structure
pfamhmmread	Read data from PFAM HMM-formatted file
showhmmprof	Plot hidden Markov model (HMM) profile

Microarray File Formats

affyprobeseqread	Read data file containing probe sequence information for Affymetrix^® GeneChip^® array
affyread	Read microarray data from Affymetrix^® GeneChip^® file
agferead	Read Agilent^® Feature Extraction Software file
celintensityread	Read probe intensities from Affymetrix^® CEL files
galread	Read microarray data from GenePix^® array list file
geosoftread	Read Gene Expression Omnibus (GEO) SOFT format data
getgeodata	Retrieve Gene Expression Omnibus (GEO) SOFT format data
gprread	Read microarray data from GenePix^® Results (GPR) file
ilmnbsread	Read gene expression data exported from Illumina^® BeadStudio™ software
imageneread	Read microarray data from ImaGene^® Results file
sptread	Read data from SPOT file

Microarray Utility

affysnpquartets	Create table of SNP probe quartet results for Affymetrix^® probe set
ilmnbslookup	Look up Illumina^® BeadStudio™ target (probe) sequence and annotation information
magetfield	Extract data from microarray structure
probelibraryinfo	Create table of probe set library information
probesetlink	Display probe set information on NetAffx™ Web site
probesetlookup	Look up information for Affymetrix^® probe set
probesetplot	Plot Affymetrix^® probe set intensity values
probesetvalues	Create table of Affymetrix^® probe set intensity values

Microarray Data Analysis and Visualization

cghcbs	Perform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data
cghfreqplot	Display frequency of DNA copy number alterations across multiple samples
chromosomeplot	Plot chromosome ideogram with G-banding pattern
clustergram	Compute hierarchical clustering, display dendrogram and heat map, and create `clustergram object`
maboxplot	Create box plot for microarray data
mafdr	Estimate false discovery rate (FDR) of differentially expressed genes from two experimental conditions or phenotypes
maimage	Spatial image for microarray data
mairplot	Create intensity versus ratio scatter plot of microarray data
maloglog	Create loglog plot of microarray data
mapcaplot	Create Principal Component Analysis (PCA) plot of microarray data
mattest	Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mavolcanoplot	Create significance versus gene expression ratio (fold change) scatter plot of microarray data
redbluecmap	Create red and blue colormap
redgreencmap	Create red and green colormap

Microarray Normalization and Filtering

affyinvarsetnorm	Perform rank invariant set normalization on probe intensities from multiple Affymetrix^® CEL or DAT files
affyprobeaffinities	Compute Affymetrix^® probe affinities from their sequences and MM probe intensities
exprprofrange	Calculate range of gene expression profiles
exprprofvar	Calculate variance of gene expression profiles
gcrma	Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix^® microarray probe-level data
gcrmabackadj	Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix^® microarray probe-level data using sequence information
geneentropyfilter	Remove genes with low entropy expression values
genelowvalfilter	Remove gene profiles with low absolute values
generangefilter	Remove gene profiles with small profile ranges
genevarfilter	Filter genes with small profile variance
mainvarsetnorm	Perform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
malowess	Smooth microarray data using Lowess method
manorm	Normalize microarray data
quantilenorm	Quantile normalization over multiple arrays
rmabackadj	Perform background adjustment on Affymetrix^® microarray probe-level data using Robust Multi-array Average (RMA) procedure
rmasummary	Calculate gene (probe set) expression values from Affymetrix^® microarray probe-level data using Robust Multi-array Average (RMA) procedure
zonebackadj	Perform background adjustment on Affymetrix^® microarray probe-level data using zone-based method

Statistical Learning

classperf	Evaluate performance of classifier
crossvalind	Generate cross-validation indices
knnclassify	Classify data using nearest neighbor method
knnimpute	Impute missing data using nearest-neighbor method
optimalleaforder	Determine optimal leaf ordering for hierarchical binary cluster tree
randfeatures	Generate randomized subset of features
rankfeatures	Rank key features by class separability criteria
samplealign	Align two data sets containing sequential observations by introducing gaps
svmclassify	Classify data using support vector machine
svmsmoset	Create or edit Sequential Minimal Optimization (SMO) options structure
svmtrain	Train support vector machine classifier

Mass Spectrometry File Formats, Preprocessing, and Visualization

jcampread	Read JCAMP-DX-formatted files
msalign	Align peaks in mass spectrum to reference peaks
msbackadj	Correct baseline of mass spectrum
msdotplot	Plot set of peak lists from LC/MS or GC/MS data set
msheatmap	Create pseudocolor image of set of mass spectra
mslowess	Smooth mass spectrum using nonparametric method
msnorm	Normalize set of mass spectra
mspalign	Align mass spectra from multiple peak lists from LC/MS or GC/MS data set
mspeaks	Convert raw mass spectrometry data to peak list (centroided data)
msppresample	Resample mass spectrometry signal while preserving peaks
msresample	Resample mass spectrometry signal
mssgolay	Smooth mass spectrum with least-squares polynomial
msviewer	Explore mass spectrum or set of mass spectra
mzxml2peaks	Convert mzXML structure to peak list
mzxmlread	Read data from mzXML file
samplealign	Align two data sets containing sequential observations by introducing gaps

Functions — Alphabetical List