Positive sample only learning (PSOL) for predicting RNA genes in E. coli

Richard F. Meraz; Xiaofeng He; Chris H.Q. Ding; Stephen R. Holbrook

Positive sample only learning (PSOL) for predicting RNA genes in E. coli

Richard F. Meraz^*
, Xiaofeng He
, Chris H.Q. Ding
, Stephen R. Holbrook

^*Corresponding author for this work

Lawrence Berkeley National Laboratory

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

RNA genes lack most of the signals used for protein gene identification. A major shortcoming of previous discriminative methods to distinguish functional RNA (fRNA) genes from other non-coding genomic sequences is that only positive examples of fRNAs are known; there are no confirmed negatives - only intergenic sequences that may be positive or negative. To address this problem we developed the "Positive Sample Only Learning" (PSOL) method. This method can identify the most likely negative examples from an unlabeled set and is therefore able to distinguish putative functional RNA genes from other non-coding sequence. We compare RNA gene predictions using the PSOL method with previous large-scale analyses of the E. coli K12 genome.

Original language	English
Title of host publication	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages	535-538
Number of pages	4
State	Published - 2004
Externally published	Yes
Event	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States Duration: 16 Aug 2004 → 19 Aug 2004

Publication series

Name	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

Conference	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Country/Territory	United States
City	Stanford, CA
Period	16/08/04 → 19/08/04

Cite this

@inproceedings{7628f5f9466b4bf2969b0b0e09b78ce9,

title = "Positive sample only learning (PSOL) for predicting RNA genes in E. coli",

abstract = "RNA genes lack most of the signals used for protein gene identification. A major shortcoming of previous discriminative methods to distinguish functional RNA (fRNA) genes from other non-coding genomic sequences is that only positive examples of fRNAs are known; there are no confirmed negatives - only intergenic sequences that may be positive or negative. To address this problem we developed the {"}Positive Sample Only Learning{"} (PSOL) method. This method can identify the most likely negative examples from an unlabeled set and is therefore able to distinguish putative functional RNA genes from other non-coding sequence. We compare RNA gene predictions using the PSOL method with previous large-scale analyses of the E. coli K12 genome.",

author = "Meraz, \{Richard F.\} and Xiaofeng He and Ding, \{Chris H.Q.\} and Holbrook, \{Stephen R.\}",

year = "2004",

language = "英语",

isbn = "0769521940",

series = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004",

pages = "535--538",

booktitle = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004",

note = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 ; Conference date: 16-08-2004 Through 19-08-2004",

}

Meraz, RF, He, X, Ding, CHQ & Holbrook, SR 2004, Positive sample only learning (PSOL) for predicting RNA genes in E. coli. in Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, pp. 535-538, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, United States, 16/08/04.

Positive sample only learning (PSOL) for predicting RNA genes in E. coli. / Meraz, Richard F.; He, Xiaofeng; Ding, Chris H.Q. et al.
Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. p. 535-538 (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Positive sample only learning (PSOL) for predicting RNA genes in E. coli

AU - Meraz, Richard F.

AU - He, Xiaofeng

AU - Ding, Chris H.Q.

AU - Holbrook, Stephen R.

PY - 2004

Y1 - 2004

N2 - RNA genes lack most of the signals used for protein gene identification. A major shortcoming of previous discriminative methods to distinguish functional RNA (fRNA) genes from other non-coding genomic sequences is that only positive examples of fRNAs are known; there are no confirmed negatives - only intergenic sequences that may be positive or negative. To address this problem we developed the "Positive Sample Only Learning" (PSOL) method. This method can identify the most likely negative examples from an unlabeled set and is therefore able to distinguish putative functional RNA genes from other non-coding sequence. We compare RNA gene predictions using the PSOL method with previous large-scale analyses of the E. coli K12 genome.

AB - RNA genes lack most of the signals used for protein gene identification. A major shortcoming of previous discriminative methods to distinguish functional RNA (fRNA) genes from other non-coding genomic sequences is that only positive examples of fRNAs are known; there are no confirmed negatives - only intergenic sequences that may be positive or negative. To address this problem we developed the "Positive Sample Only Learning" (PSOL) method. This method can identify the most likely negative examples from an unlabeled set and is therefore able to distinguish putative functional RNA genes from other non-coding sequence. We compare RNA gene predictions using the PSOL method with previous large-scale analyses of the E. coli K12 genome.

UR - https://www.scopus.com/pages/publications/14044278169

M3 - 会议稿件

AN - SCOPUS:14044278169

SN - 0769521940

SN - 9780769521947

T3 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

SP - 535

EP - 538

BT - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

T2 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Y2 - 16 August 2004 through 19 August 2004

ER -

Positive sample only learning (PSOL) for predicting RNA genes in E. coli

Abstract

Publication series

Conference

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