| Bioinformatics Toolbox™ | |
FASTAData = fastaread(File)
[Header, Sequence] = fastaread(File)
... = fastaread(File,
...'IgnoreGaps', IgnoreGapsValue, ...)
... = fastaread(File, ...'Blockread', BlockreadValue,
...)
| File | FASTA-formatted file (ASCII text file). Enter a file name, a path and file name, or a URL pointing to a file. File can also be a MATLAB® character array that contains the text for a file name. |
| IgnoreGapsValue | Property to control removing gap symbols. Enter either true or false (default). |
| BlockreadValue | Property to control reading a single entry or block of entries from a file containing multiple sequences. Enter a scalar N, to read the Nth entry in the file. Enter a 1-by-2 vector [M1, M2], to read the block of entries starting at entry M1 and ending at entry M2. To read all remaining entries in the file starting at entry M1, enter a positive value for M1 and enter Inf for M2. |
| FASTAData | MATLAB structure with the fields Header and Sequence. |
fastaread reads data from a FASTA-formatted file into a MATLAB structure with the following fields.
| Field |
|---|
| Header |
| Sequence |
A file with a FASTA format begins with a right angle bracket (>) and a single line description. Following this description is the sequence as a series of lines with fewer than 80 characters. Sequences are expected to use the standard IUB/IUPAC amino acid and nucleotide letter codes.
For a list of codes, see aminolookup and baselookup.
FASTAData = fastaread(File) reads a file with a FASTA format and returns the data in a structure. FASTAData.Header is the header information, while FASTAData.Sequence is the sequence stored as a string of letters.
[Header, Sequence] = fastaread(File) reads data from a file into separate variables. If the file contains more than one sequence, then header and sequence are cell arrays of header and sequence information.
... = fastaread(File, ...'PropertyName', PropertyValue, ...) calls fastaread with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. The property name/value pairs can be in any format supported by the function set (for example, name-value string pairs, structures, and name-value cell array pairs). These property name/property value pairs are as follows:
... = fastaread(File,
...'IgnoreGaps', IgnoreGapsValue, ...),
when IgnoreGapsValue is true,
removes any gap symbol ('-' or '.')
from the sequences. Default is false.
... = fastaread(File, ...'Blockread', BlockreadValue, ...) lets you read in a single entry or block of entries from a file containing multiple sequences. If BlockreadValue is a scalar N, then fastaread reads the Nth entry in the file. If BlockreadValue is a 1-by-2 vector [M1, M2], then fastaread reads the block of entries starting at entry M1 and ending at entry M2. To read all remaining entries in the file starting at entry M1, enter a positive value for M1 and enter Inf for M2.
Read the sequence for the human p53 tumor gene.
p53nt = fastaread('p53nt.txt')Read the sequence for the human p53 tumor protein.
p53aa = fastaread('p53aa.txt')Read the human mitochondrion genome in FASTA format.
entrezSite = 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?' textOptions = '&txt=on&view=fasta' genbankID = '&list_uids=NC_001807' mitochondrion = fastaread([entrezSite textOptions genbankID])
Bioinformatics Toolbox™ functions: emblread, fastawrite, genbankread, genpeptread, multialignread, seqprofile, seqtool
| exprprofvar | fastawrite | |
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