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API Docs / SMRUCC.genomics.Core / UniprotFasta

UniprotFasta

Full name SMRUCC.genomics.Assembly.Uniprot.UniprotFasta Assembly SMRUCC.genomics.Core Members 6

A fasta object which is specific for the uniprot fasta title parsing.(专门用于解析Uniprot蛋白质序列记录的Fasta对象)

The following is a description of FASTA headers for UniProtKB (including alternative isoforms), UniRef, UniParc and archived UniProtKB versions. NCBI's program formatdb (in particular its -o option) is compatible with the UniProtKB fasta headers.

UniProtKB

db|UniqueIdentifier|EntryName ProteinName OS=OrganismName[ GN=GeneName]PE=ProteinExistence SV=SequenceVersion

Where: db Is 'sp' for UniProtKB/Swiss-Prot and 'tr' for UniProtKB/TrEMBL. UniqueIdentifier Is the primary accession number of the UniProtKB entry. EntryName Is the entry name of the UniProtKB entry. ProteinName Is the recommended name of the UniProtKB entry as annotated in the RecName field. For UniProtKB/TrEMBL entries without a RecName field, the SubName field Is used. In case of multiple SubNames, the first one Is used. The 'precursor' attribute is excluded, 'Fragment' is included with the name if applicable. OrganismName Is the scientific name of the organism of the UniProtKB entry. GeneName Is the first gene name of the UniProtKB entry. If there Is no gene name, OrderedLocusName Or ORFname, the GN field Is Not listed. ProteinExistence Is the numerical value describing the evidence for the existence of the protein. SequenceVersion Is the version number of the sequence.

00 Remarks

http://www.uniprot.org/help/fasta-headers

01 Syntax

SMRUCC.genomics.Assembly.Uniprot.UniprotFasta

02 Methods

NameOverloadsSummary
CreateObject 1 从读取的文件数据之中创建一个Uniprot序列对象
ParseHeader 1 Parse the fasta header of the sequence from UniProt database.
LoadFasta 1 Load the uniprot fasta sequence file.
SimpleHeaderParser 1

03 Properties

NameOverloadsSummary
UniprotID 1
UniProtHeader 1

04 Members

method CreateObject #
CreateObject(FastaSeq)

从读取的文件数据之中创建一个Uniprot序列对象

Remarks

sp|Q197F8|002R_IIV3 Uncharacterized protein 002R OS=Invertebrate iridescent virus 3 GN=IIV3-002R PE=4 SV=1

Parameters
NameTypeDescription
fastaFastaSeq

-

method ParseHeader #
ParseHeader(String, String)

Parse the fasta header of the sequence from UniProt database.

Parameters
NameTypeDescription
sString

-

idString

-

method LoadFasta #
LoadFasta(String)

Load the uniprot fasta sequence file.

Parameters
NameTypeDescription
pathString

-

property UniprotID #
UniprotID
property UniProtHeader #
UniProtHeader
method SimpleHeaderParser #
SimpleHeaderParser(String)