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 |
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.