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SPD--a web-based secreted protein database.

Abstract：

:With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They were further annotated via a proteome annotation pipeline that we developed. We also set up a secreted protein classification pipeline and classified our predicted secreted proteins into different functional categories. To make the dataset more convincing and comprehensive, nine reference datasets are also integrated, such as the secreted proteins from the Gene Ontology Annotation (GOA) system at the European Bioinformatics Institute, and the vertebrate secreted proteins from Swiss-Prot. All these entries were grouped via a TribeMCL based clustering pipeline. We have constructed a web-based secreted protein database, which has been publicly available at http://spd.cbi.pku.edu.cn. Users can browse the database via a GO assignment or chromosomal-location-based interface. Moreover, text query and sequence similarity search are also provided, and the sequence and annotation data can be downloaded freely from the SPD website.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Chen Y,Zhang Y,Yin Y,Gao G,Li S,Jiang Y,Gu X,Luo J

doi

10.1093/nar/gki093

keywords:

subject

Has Abstract

pub_date

2005-01-01 00:00:00

pages

D169-73

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

33/suppl_1/D169

journal_volume

33

pub_type

杂志文章

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