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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


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
blastreadlocal Read data from local BLAST report
blastformat Create local BLAST database
getblast Retrieve BLAST report from NCBI Web site
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

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.


Data Formats and Databases

The Bioinformatics Toolbox™ accesses many of the databases on the Web and other online data sources.

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