PlantProm: A database of plant promoter sequences

Ilham A. Shahmuradov; Alex J. Gammerman; John M. Hancock; Peter M. Bramley; Victor V. Solovyev

doi:10.1093/nar/gkg041

PlantProm: A database of plant promoter sequences

Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, Victor V. Solovyev^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

231 Scopus citations

Abstract

PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species. The first release (2002.01) of PlantProm DB contains 305 entries including 71, 220 and 14 promoters from monocot, dicot and other plants, respectively. It provides DNA sequence of the promoter regions (-200:+51) with TSS on the fixed position +201, taxonomic/promoter type classification of promoters and Nucleotide Frequency Matrices (NFM) for promoter elements: TATA-box, CCAAT-box and TSS-motif (Inr). Analysis of TSS-motifs revealed that their composition is different in dicots and monocots, as well as for TATA and TATA-less promoters. The database serves as learning set in developing plant promoter prediction programs. One such program (TSSP) based on discriminant analysis has been created by Softberry Inc. and the application of a support vector machine approach for promoter identification is under development. PlantProm DB is available at http://mendel.cs.rhul.ac.uk/ and http://www.softberry.com/.

Original language	English (US)
Pages (from-to)	114-117
Number of pages	4
Journal	NUCLEIC ACIDS RESEARCH
Volume	31
Issue number	1
DOIs	https://doi.org/10.1093/nar/gkg041
State	Published - Jan 1 2003
Externally published	Yes

Bibliographical note

Funding Information:
PlantProm DB is funded by grant 111/BIO14428 ‘Pattern Recognition Techniques for Gene Identification in Plant Genomic Sequences’, from the UK Biotechnology and Biological Sciences Research Council (BBSRC) and is designed and maintained at Royal Holloway, University of London in collaboration with Softberry Inc. (USA).

ASJC Scopus subject areas

Genetics

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title = "PlantProm: A database of plant promoter sequences",

abstract = "PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species. The first release (2002.01) of PlantProm DB contains 305 entries including 71, 220 and 14 promoters from monocot, dicot and other plants, respectively. It provides DNA sequence of the promoter regions (-200:+51) with TSS on the fixed position +201, taxonomic/promoter type classification of promoters and Nucleotide Frequency Matrices (NFM) for promoter elements: TATA-box, CCAAT-box and TSS-motif (Inr). Analysis of TSS-motifs revealed that their composition is different in dicots and monocots, as well as for TATA and TATA-less promoters. The database serves as learning set in developing plant promoter prediction programs. One such program (TSSP) based on discriminant analysis has been created by Softberry Inc. and the application of a support vector machine approach for promoter identification is under development. PlantProm DB is available at http://mendel.cs.rhul.ac.uk/ and http://www.softberry.com/.",

author = "Shahmuradov, {Ilham A.} and Gammerman, {Alex J.} and Hancock, {John M.} and Bramley, {Peter M.} and Solovyev, {Victor V.}",

note = "Funding Information: PlantProm DB is funded by grant 111/BIO14428 {\textquoteleft}Pattern Recognition Techniques for Gene Identification in Plant Genomic Sequences{\textquoteright}, from the UK Biotechnology and Biological Sciences Research Council (BBSRC) and is designed and maintained at Royal Holloway, University of London in collaboration with Softberry Inc. (USA).",

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AU - Shahmuradov, Ilham A.

AU - Gammerman, Alex J.

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AU - Bramley, Peter M.

AU - Solovyev, Victor V.

N1 - Funding Information: PlantProm DB is funded by grant 111/BIO14428 ‘Pattern Recognition Techniques for Gene Identification in Plant Genomic Sequences’, from the UK Biotechnology and Biological Sciences Research Council (BBSRC) and is designed and maintained at Royal Holloway, University of London in collaboration with Softberry Inc. (USA).

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N2 - PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species. The first release (2002.01) of PlantProm DB contains 305 entries including 71, 220 and 14 promoters from monocot, dicot and other plants, respectively. It provides DNA sequence of the promoter regions (-200:+51) with TSS on the fixed position +201, taxonomic/promoter type classification of promoters and Nucleotide Frequency Matrices (NFM) for promoter elements: TATA-box, CCAAT-box and TSS-motif (Inr). Analysis of TSS-motifs revealed that their composition is different in dicots and monocots, as well as for TATA and TATA-less promoters. The database serves as learning set in developing plant promoter prediction programs. One such program (TSSP) based on discriminant analysis has been created by Softberry Inc. and the application of a support vector machine approach for promoter identification is under development. PlantProm DB is available at http://mendel.cs.rhul.ac.uk/ and http://www.softberry.com/.

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PlantProm: A database of plant promoter sequences

Abstract

Bibliographical note

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