| Bioinformatics Toolbox | |
Retrieve sequence data from PIR-PSD database
Data = getpir('AccessionNumber',
'PropertyName', PropertyValue...)
getpir(..., 'ToFile', ToFileValue)
getpir(..., 'SequenceOnly', SequenceOnlyValue)
AccessionNumber | Unique identifier for a sequence record. Enter a unique combination of letters and numbers. |
ToFile | Property to specify the location and filename for saving data. Enter either a filename or a path and filename supported by your system. |
SequenceOnly | Property to control getting the sequence only. Enter either true or false. |
Data = getpir('AccessionNumber', 'PropertyName',PropertyValue...) searches for the accession number in the PIR-PSD database, and returns a MATLAB structure containing the following fields:
Entry EntryType Title Organism Date Accessions Reference Genetics Classification Keywords Feature Summary Sequence
getpir(..., 'ToFile', ToFileValue) saves the data retrieved from the PIR-PSD database in a file. Read a PIR-PSD formatted file back into MATLAB using the function pirread.
getpir(..., 'SequenceOnly', SequenceOnlyValue) returns only the sequence information for the protein as a string if SequenceOnly is true.
The Protein Sequence Database (PIR-PSD) is maintained by the Protein Information Resource (PIR) division of the National Biomedical Research Foundation (NBRF), which is affiliated with Georgetown University Medical Center.
Return a structure, pirdata, that holds the result of a query into the PIR-PSD database using 'cchu' as the search string.
pirdata = getpir('cchu')
pirdata =
Entry: 'CCHU'
EntryType: 'complete'
Title: 'cytochrome c [validated] - human'
Organism: [1x1 struct]
Date: [1x1 struct]
Accessions: 'A31764; A05676; I55192; A00001'
Reference: {[1x1 struct] [1x1 struct] [1x1 struct]
[1x1 struct]}
Genetics: {[1x1 struct]}
Classification: [1x1 struct]
Keywords: [1x157 char]
Feature: {1x5 cell}
Summary: [1x1 struct]
Sequence: [1x105 char]
Return a string, pirdata, that holds the sequence information for the query 'cchu' in the PIR-PSD database.
pirseq = getpir('cchu','SequenceOnly',true)
Return a structure, pirdata, that holds the result of a query into the PIR database using 'cchu' as the search string. It also creates a text file, cchu.pir, in the current folder that holds the data retrieved from the PIR database. Note that the entire data retrieved from the database is stored in ToFileValue even if SequenceOnly is true.
pirdata = getpir('cchu', 'ToFile','cchu.pir')
Bioinformatics Toolbox functions genpeptread, getgenpept, getpdb, pdbread, pirread
| | getpdb | getrelatives (biograph) | |
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