A VOM based gene-finder that specializes in short genes

Keren Or Shohat-Zaidenraise; Armin Shmilovici; Irad Ben-Gal

A VOM based gene-finder that specializes in short genes

Keren Or Shohat-Zaidenraise, Armin Shmilovici, Irad Ben-Gal

Department of Software and Information Systems Engineering

Research output: Contribution to conference › Paper › peer-review

1 Scopus citations

Abstract

We present a new approach for gene finding based on a Variable-Order Markov (VOM) Model. The VOM model is a generalization of the traditional Markov model, which is more efficient in terms of its parameterization, thus, can be trained on relatively short sequences. As a result, the proposed VOM gene-finder outperforms traditional gene-finders that are based on fifth-order Markov models for short newly sequenced bacterial genomes.

Original language	English
Pages	189-192
Number of pages	4
State	Published - 1 Dec 2004
Event	2004 23rd IEEE Convention of Electrical and Electronics Engineers in Israel, Proceedings - Tel-Aviv, Israel Duration: 6 Sep 2004 → 7 Sep 2004

Conference

Conference	2004 23rd IEEE Convention of Electrical and Electronics Engineers in Israel, Proceedings
Country/Territory	Israel
City	Tel-Aviv
Period	6/09/04 → 7/09/04

Keywords

Gene Finding
Sequence Analysis
Variable Order Markov Models

ASJC Scopus subject areas

Electrical and Electronic Engineering
Electronic, Optical and Magnetic Materials

Cite this

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title = "A VOM based gene-finder that specializes in short genes",

abstract = "We present a new approach for gene finding based on a Variable-Order Markov (VOM) Model. The VOM model is a generalization of the traditional Markov model, which is more efficient in terms of its parameterization, thus, can be trained on relatively short sequences. As a result, the proposed VOM gene-finder outperforms traditional gene-finders that are based on fifth-order Markov models for short newly sequenced bacterial genomes.",

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AU - Shmilovici, Armin

AU - Ben-Gal, Irad

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N2 - We present a new approach for gene finding based on a Variable-Order Markov (VOM) Model. The VOM model is a generalization of the traditional Markov model, which is more efficient in terms of its parameterization, thus, can be trained on relatively short sequences. As a result, the proposed VOM gene-finder outperforms traditional gene-finders that are based on fifth-order Markov models for short newly sequenced bacterial genomes.

AB - We present a new approach for gene finding based on a Variable-Order Markov (VOM) Model. The VOM model is a generalization of the traditional Markov model, which is more efficient in terms of its parameterization, thus, can be trained on relatively short sequences. As a result, the proposed VOM gene-finder outperforms traditional gene-finders that are based on fifth-order Markov models for short newly sequenced bacterial genomes.

KW - Gene Finding

KW - Sequence Analysis

KW - Variable Order Markov Models

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M3 - Paper

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T2 - 2004 23rd IEEE Convention of Electrical and Electronics Engineers in Israel, Proceedings

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ER -

A VOM based gene-finder that specializes in short genes

Abstract

Conference

Keywords

ASJC Scopus subject areas

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Cite this