Bioinformatics Toolbox™

genpeptread - Read data from GenPept file

Syntax

GenPeptData = genpeptread('File')

Arguments

File GenPept 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 of a GenPept file.

Description

genpeptread reads data from a GenPept formatted file into a MATLAB structure.

Note NCBI has changed the name of their protein search engine from GenPept to Entrez Protein. However, the function names in the Bioinformatics Toolbox software (getgenpept and genpeptread) are unchanged representing the still-used GenPept report format.

GenPeptData = genpeptread('File') reads in the GenPept formatted sequence from File and creates a structure GenPeptData, containing fields corresponding to the GenPept keywords. Each separate sequence listed in File is stored as a separate element of the structure. GenPeptDATA contains these fields:

Field
`LocusName`
`LocusSequenceLength`
`LocusMoleculeType`
`LocusGenBankDivision`
`LocusModificationDate`
`Definition`
`Accession`
`PID`
`Version`
`GI`
`DBSource`
`Keywords`
`Source`
`SourceDatabase`
`SourceOrganism`
`Reference.Number`
`Reference.Authors`
`Reference.Title`
`Reference.Journal`
`Reference.MedLine`
`Reference.PubMed`
`Reference.Remark`
`Comment`
`Features`
`Weight`
`Length`
`Sequence`

Examples

Retrieve sequence information for the protein coded by the gene HEXA, save to a file, and then read back into the MATLAB software.

getgenpept('p06865', 'ToFile', 'TaySachs_Protein.txt')
genpeptread('TaySachs_Protein.txt')

genpeptread - Read data from GenPept file

Syntax

Arguments

Description

Examples

See Also