Data Import and Export
Import data in various formats, including FASTA, GenBank, GenPept, EMBL, BLAST, PDB, PFAM, ClustalW, GCG, PHYLIP, Newick, and FASTQ, from public repositories and local file systems; write to various formats, including FASTA, PDB, and Newick
Import data from public databases, such as GenBank and EMBL, and use it for further analyses within MATLAB. Load data from various file formats including FASTA, FASTQ, GenBank, EMBL, and BLAST. You can also save the results to various file formats.
|Return information about FASTA file|
|Read data from FASTA file|
|Write to file using FASTA format|
|Return information about FASTQ file|
|Read data from FASTQ file|
|Write to file using FASTQ format|
GenBank, EMBL, and PDB
|Read data from GenBank file|
|Retrieve sequence information from GenBank database|
|Read data from GenPept file|
|Retrieve sequence information from GenPept database|
|Read data from EMBL file|
|Retrieve sequence information from EMBL database|
|Read data from Protein Data Bank (PDB) file|
|Write to file using Protein Data Bank (PDB) format|
|Retrieve protein structure data from Protein Data Bank (PDB) database|
ClustalW, GCG, and PHYLIP
|Read data from PFAM HMM-formatted file|
|Retrieve hidden Markov model (HMM) profile from PFAM database|
|Retrieve phylogenetic tree data from PFAM database|
|Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database|
|Read phylogenetic tree file|
|Write phylogenetic tree object to Newick-formatted file|
- 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.