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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

fastainfoReturn information about FASTA file
fastareadRead data from FASTA file
fastawriteWrite to file using FASTA format
genbankreadRead data from GenBank file
getgenbankRetrieve sequence information from GenBank database
genpeptreadRead data from GenPept file
getgenpeptRetrieve sequence information from GenPept database
emblreadRead data from EMBL file
getemblRetrieve sequence information from EMBL database
pdbreadRead data from Protein Data Bank (PDB) file
pdbwriteWrite to file using Protein Data Bank (PDB) format
getpdbRetrieve protein structure data from Protein Data Bank (PDB) database
fastqinfoReturn information about FASTQ file
fastqreadRead data from FASTQ file
fastqwriteWrite to file using FASTQ format
blastreadRead data from NCBI BLAST report file
blastreadlocalRead data from local BLAST report
blastformatCreate local BLAST database
getblastRetrieve BLAST report from NCBI website
multialignreadRead multiple sequence alignment file
multialignwriteWrite multiple alignment to file
pfamhmmreadRead data from PFAM HMM-formatted file
gethmmprofRetrieve hidden Markov model (HMM) profile from PFAM database
gethmmtreeRetrieve phylogenetic tree data from PFAM database
gethmmalignmentRetrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
phytreereadRead phylogenetic tree file
phytreewriteWrite phylogenetic tree object to Newick-formatted file

Examples and How To

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.

Concepts

Data Formats and Databases

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

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