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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.


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fastainfoReturn information about FASTA file
fastareadRead data from FASTA file
fastawriteWrite to file using FASTA format
fastqinfoReturn information about FASTQ file
fastqreadRead data from FASTQ file
fastqwriteWrite to file using FASTQ 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
blastplusSearch local BLAST+ database (Since R2024a)
blastplusdatabaseCreate a local BLAST+ database (Since R2024a)
blastreadRead data from NCBI BLAST report file
getblastRetrieve BLAST report from NCBI website
blastplusoptionsCreate options for BLAST query program (Since R2024a)
MakeDatabaseOptionsSpecify options to make BLAST database (Since R2024a)
resetReset BLAST database options to default values (Since R2024a)
bioinfo.blastplus.BLASTNOptionsSpecify options for blastn query program (Since R2024a)
bioinfo.blastplus.BLASTPOptionsSpecify options for blastp query program (Since R2024a)
bioinfo.blastplus.BLASTXOptionsSpecify options for blastx query program (Since R2024a)
bioinfo.blastplus.TBLASTNOptionsContain options for tblastn query program (Since R2024a)
bioinfo.blastplus.TBLASTXOptionsContain options for tblastx query program (Since R2024a)
bioinfo.blastplus.DefaultDefault value set by BLAST program or task (Since R2024a)
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