pTARGET: A web server for predicting protein subcellular localization

Chittibabu Guda

doi:10.1093/nar/gkl093

pTARGET: A web server for predicting protein subcellular localization

Chittibabu Guda

Research output: Contribution to journal › Article › peer-review

52 Scopus citations

Abstract

The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963-3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/ ~ptarget.

Original language	English (US)
Pages (from-to)	W210-W213
Journal	Nucleic acids research
Volume	34
Issue number	WEB. SERV. ISS.
DOIs	https://doi.org/10.1093/nar/gkl093
State	Published - Jul 2006
Externally published	Yes

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gkl093

Cite this

@article{32465e5d33374a2c81296d9f53d7ba6c,

title = "pTARGET: A web server for predicting protein subcellular localization",

abstract = "The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963-3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/ ~ptarget.",

author = "Chittibabu Guda",

note = "Funding Information: This work has been supported by the startup funds to CG from the State University of New York at Albany (SUNY, Albany). The author is thankful to Research IT staff at SUNY, Albany and to Dr Russ Miller{\textquoteright}s group at SUNY, Buffalo for providing access to grid computing to run large-scale HMMER jobs. Funding to pay the Open Access publication charges for this article was provided by the SUNY startup funds.",

year = "2006",

month = jul,

doi = "10.1093/nar/gkl093",

language = "English (US)",

volume = "34",

pages = "W210--W213",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "WEB. SERV. ISS.",

}

TY - JOUR

T1 - pTARGET

T2 - A web server for predicting protein subcellular localization

AU - Guda, Chittibabu

N1 - Funding Information: This work has been supported by the startup funds to CG from the State University of New York at Albany (SUNY, Albany). The author is thankful to Research IT staff at SUNY, Albany and to Dr Russ Miller’s group at SUNY, Buffalo for providing access to grid computing to run large-scale HMMER jobs. Funding to pay the Open Access publication charges for this article was provided by the SUNY startup funds.

PY - 2006/7

Y1 - 2006/7

N2 - The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963-3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/ ~ptarget.

AB - The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963-3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/ ~ptarget.

UR - http://www.scopus.com/inward/record.url?scp=33747375161&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33747375161&partnerID=8YFLogxK

U2 - 10.1093/nar/gkl093

DO - 10.1093/nar/gkl093

M3 - Article

C2 - 16844995

AN - SCOPUS:33747375161

SN - 0305-1048

VL - 34

SP - W210-W213

JO - Nucleic acids research

JF - Nucleic acids research

IS - WEB. SERV. ISS.

ER -

pTARGET: A web server for predicting protein subcellular localization

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this