[BioPython] Bio.SwissProt

0. SwissProt이란 단백질 데이터베이스라고한다. 

이번장에서는 SwissProt을 Biopython을 이용해 사용하는 방법을 다루고자한다. 

 

1. 사용법 

from Bio import SwissProt 
handle = open(file path) 
record = SwissProt.read(handle) 
print(type(record)) 
handle.close()

output 

<class 'Bio.SwissProt.Record'>

 

2. Swiss-Prot.record 객체를 parsing하기 

SwissProt.Record 객체를 생성하면, SwissProt 파일에대한 정보가 record에 담겨있다. 따라서, 필요한 정보를 가져오면된다.

from Bio import SwissProt 
handle = open("../swissprot/P02649.txt") 
record = SwissProt.read(handle) 
print(type(record)) 
handle.close() 

print(record.description) 
print("gene_name :", record.gene_name) 
print("organism : ", record.organism) 
print("sequence_length : ", record.sequence_length) 
print("sequence : ", record.sequence)

 

output

<class 'Bio.SwissProt.Record'>
RecName: Full=Apolipoprotein E {ECO:0000305}; Short=Apo-E; Flags: Precursor;
gene_name : [{'Name': 'APOE {ECO:0000312|HGNC:HGNC:613}'}]
organism :  Homo sapiens (Human).
sequence_length :  317
sequence :  MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMGSRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEKVQAAVGTSAAPVPSDNH

 

 

3. ExPASy 

ExPASy란 Swiss-Prot 데이터를 가지고있는 서버다. 또한, 단백질체학툴도 들어있다고한다.

It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.

출처 : https://www.expasy.org/about

About Expasy - SIB Swiss Institute of Bioinformatics | Expasy

from Bio import SwissProt 
from Bio import ExPASy 

accession = "P02649" 
handle = ExPASy.get_sprot_raw(accession) 
record = SwissProt.read(handle) 
print(record.gene_name) 
print(record.organism) 
print(record.sequence_length) 
print(record.sequence)

 

output

[{'Name': 'APOE {ECO:0000312|HGNC:HGNC:613}'}]
Homo sapiens (Human).
317
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVYQAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMGSRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEKVQAAVGTSAAPVPSDNH

 

 

4. 활용

from Bio import SwissProt,ExPASy 

accession = "P05067" 
handle = ExPASy.get_sprot_raw(accession) 
record = SwissProt.read(handle) 
print(record.gene_name) 
print(record.organism) 
print(record.sequence_length) 
print(record.sequence)

 

output

[{'Name': 'APP {ECO:0000312|HGNC:HGNC:620}', 'Synonyms': ['A4 {ECO:0000303|PubMed:2881207}', 'AD1 {ECO:0000312|HGNC:HGNC:620}']}]
Homo sapiens (Human).
770
MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN