| Bioinformatics Toolbox | |
The Bioinformatics Toolbox supports access to many of the databases on the Web and other online data sources. It also reads many common genome file formats, so that you do not have to write and maintain your own file readers.
Web-based databases — You can directly access public databases on the Web and copy sequence and gene expression information into MATLAB.
The sequence databases currently supported are GenBank (getgenbank), GenPept (getgenpept), European Molecular Biology Laboratory EMBL (getembl), Protein Sequence Database PIR-PSD (getpir), and Protein Data Bank PDB (getpdb). You can also access data from the NCBI Gene Expression Omnibus (GEO) web site by using a single function (getgeodata).
Get multiply aligned sequences (gethmmalignment), hidden Markov model profiles (gethmmprof), and phylogenetic tree data (gethmmtree) from the PFAM database.
Raw data — Read data generated from gene sequencing instruments (scfread, joinseq, traceplot) and mass spectrometers (jcampread).
Reading data formats — The toolbox provides a number of functions for reading data from common bioinformatic file formats.
Sequence data: GenBank (genbankread), GenPept (genpeptread), EMBL (emblread), PIR-PSD (pirread), PDB (pdbread), and FASTA (fastaread)
Multiply aligned sequences: ClustalW and GCG formats (multialignread)
Gene expression data from microarrays: Gene Expression Omnibus (GEO) data ( ), GenePix data in GPR and GAL files (gprread, galread), SPOT data (sptread), and Affymetrix data (affyread)
Note: The function affyread only works on PC supported platforms.
Hidden Markov model profiles: PFAM-HMM file (pfamhmmread)
Writing data formats — The functions for getting data from the Web include the option to save the data to a file. However, there is a function to write data to a file using the FASTA format (fastawrite).
BLAST searches — Request Web-based BLAST searches (blastncbi), get the results from a search (getblast) and read results from a previously saved BLAST formatted report file (blastread).
MATLAB has built-in support for other industry-standard file formats including Microsoft Excel and comma-separated value (CSV) files. Additional functions perform ASCII and low-level binary I/O, allowing you to develop custom functions for working with any data format.
| | Features and Functions | Sequence Alignments | |
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