NDLI: Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction

Content Provider	Springer Nature Link
Author	Shen, H. B. Yang, J. Chou, K. C.
Copyright Year	2007
Abstract	With the avalanche of newly-found protein sequences emerging in the post genomic era, it is highly desirable to develop an automated method for fast and reliably identifying their subcellular locations because knowledge thus obtained can provide key clues for revealing their functions and understanding how they interact with each other in cellular networking. However, predicting subcellular location of eukaryotic proteins is a challenging problem, particularly when unknown query proteins do not have significant homology to proteins of known subcellular locations and when more locations need to be covered. To cope with the challenge, protein samples are formulated by hybridizing the information derived from the gene ontology database and amphiphilic pseudo amino acid composition. Based on such a representation, a novel ensemble hybridization classifier was developed by fusing many basic individual classifiers through a voting system. Each of these basic classifiers was engineered by the KNN (K-Nearest Neighbor) principle. As a demonstration, a new benchmark dataset was constructed that covers the following 18 localizations: (1) cell wall, (2) centriole, (3) chloroplast, (4) cyanelle, (5) cytoplasm, (6) cytoskeleton, (7) endoplasmic reticulum, (8) extracell, (9) Golgi apparatus, (10) hydrogenosome, (11) lysosome, (12) mitochondria, (13) nucleus, (14) peroxisome, (15) plasma membrane, (16) plastid, (17) spindle pole body, and (18) vacuole. To avoid the homology bias, none of the proteins included has ≥25% sequence identity to any other in a same subcellular location. The overall success rates thus obtained via the 5-fold and jackknife cross-validation tests were 81.6 and 80.3%, respectively, which were 40–50% higher than those performed by the other existing methods on the same strict dataset. The powerful predictor, named “Euk-PLoc”, is available as a web-server at http://202.120.37.186/bioinf/euk . Furthermore, to support the need of people working in the relevant areas, a downloadable file will be provided at the same website to list the results predicted by Euk-PLoc for all eukaryotic protein entries (excluding fragments) in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The large-scale results will be updated twice a year to include the new entries of eukaryotic proteins and reflect the continuous development of Euk-PLoc.
Starting Page	57
Ending Page	67
Page Count	11
File Format	PDF
ISSN	09394451
Journal	Amino Acids
Volume Number	33
Issue Number	1
e-ISSN	14382199
Language	English
Publisher	Springer-Verlag
Publisher Date	2007-01-19
Publisher Place	Vienna
Access Restriction	Subscribed
Subject Keyword	Biochemistry Analytical Chemistry Biochemical Engineering Life Sciences Proteomics Neurobiology
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Biochemistry Clinical Biochemistry

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection

Predicting protein subcellular location: exploiting amino acid based sequence of feature spaces and fusion of diverse classifiers

Using ensemble classifier to identify membrane protein types

Using complexity measure factor to predict protein subcellular location

SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor

A complexity-based method for predicting protein subcellular location

Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine

PROlocalizer: integrated web service for protein subcellular localization prediction

Prediction of protein subcellular localization by support vector machines using multi-scale energy and pseudo amino acid composition

Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction

Similar Documents

Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection

Predicting protein subcellular location: exploiting amino acid based sequence of feature spaces and fusion of diverse classifiers

Using ensemble classifier to identify membrane protein types

Using complexity measure factor to predict protein subcellular location

SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor

A complexity-based method for predicting protein subcellular location

Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine

PROlocalizer: integrated web service for protein subcellular localization prediction

Prediction of protein subcellular localization by support vector machines using multi-scale energy and pseudo amino acid composition

Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction