Documentation

Data Import and Export

Import sequence data from public repositories and local file systems, including FASTA, GenBank, GenPept, EMBL, BLAST, PDB, PFAM, ClustalW, GCG, PHYLIP, Newick, and FASTQ; write to various formats, including FASTA, PDB, and Newick

Functions

`fastainfo`	Return information about FASTA file
`fastaread`	Read data from FASTA file
`fastawrite`	Write to file using FASTA format

`genbankread`	Read data from GenBank file
`getgenbank`	Retrieve sequence information from GenBank database
`genpeptread`	Read data from GenPept file
`getgenpept`	Retrieve sequence information from GenPept database
`emblread`	Read data from EMBL file
`getembl`	Retrieve sequence information from EMBL database
`pdbread`	Read data from Protein Data Bank (PDB) file
`pdbwrite`	Write to file using Protein Data Bank (PDB) format
`getpdb`	Retrieve protein structure data from Protein Data Bank (PDB) database

`fastqinfo`	Return information about FASTQ file
`fastqread`	Read data from FASTQ file
`fastqwrite`	Write to file using FASTQ format

`blastread`	Read data from NCBI BLAST report file
`getblast`	Retrieve BLAST report from NCBI website

`multialignread`	Read multiple sequence alignment file
`multialignwrite`	Write multiple alignment to file

`pfamhmmread`	Read data from PFAM HMM-formatted file
`gethmmprof`	Retrieve hidden Markov model (HMM) profile from PFAM database
`gethmmtree`	Retrieve phylogenetic tree data from PFAM database
`gethmmalignment`	Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database

`phytreeread`	Read phylogenetic tree file
`phytreewrite`	Write phylogenetic tree object to Newick-formatted file

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.

Data Formats and Databases

Access online databases and repositories using various MATLAB^® functions and import data to the workspace for further analyses.

Featured Examples

Accessing NCBI Entrez Databases with E-Utilities

Accessing NCBI Entrez Databases with E-Utilities

Programmatically search and retrieve data from NCBI's Entrez databases using NCBI's Entrez Utilities (E-Utilities).

Bioinformatics Toolbox Documentation

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