SinEx DB: a database for single exon coding sequences in mammalian genomes

Roddy Jorquera, Rodrigo Ortiz, F. Ossandon, Juan Pablo Cárdenas, Rene Sepúlveda, Carolina González, David S. Holmes

Resultado de la investigación: Article

10 Citas (Scopus)

Resumen

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.

Idioma originalEnglish
PublicaciónDatabase : the journal of biological databases and curation
Volumen2016
DOI
EstadoPublished - 1 ene 2016

Huella dactilar

exons
Exons
Genes
Genome
Databases
genome
genes
introns
Introns
nucleotide sequences
prediction
nuclear proteins
information sources
Human Genome
Nuclear Proteins
amino acid sequences
DNA
Servers
Proteins
phylogeny

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Citar esto

Jorquera, R., Ortiz, R., Ossandon, F., Cárdenas, J. P., Sepúlveda, R., González, C., & Holmes, D. S. (2016). SinEx DB: a database for single exon coding sequences in mammalian genomes. Database : the journal of biological databases and curation, 2016. https://doi.org/10.1093/database/baw095
Jorquera, Roddy ; Ortiz, Rodrigo ; Ossandon, F. ; Cárdenas, Juan Pablo ; Sepúlveda, Rene ; González, Carolina ; Holmes, David S. / SinEx DB : a database for single exon coding sequences in mammalian genomes. En: Database : the journal of biological databases and curation. 2016 ; Vol. 2016.
@article{83dfbba411ee4bf1a605b8c080aaae92,
title = "SinEx DB: a database for single exon coding sequences in mammalian genomes",
abstract = "Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.",
author = "Roddy Jorquera and Rodrigo Ortiz and F. Ossandon and C{\'a}rdenas, {Juan Pablo} and Rene Sep{\'u}lveda and Carolina Gonz{\'a}lez and Holmes, {David S.}",
year = "2016",
month = "1",
day = "1",
doi = "10.1093/database/baw095",
language = "English",
volume = "2016",
journal = "Database : the journal of biological databases and curation",
issn = "1758-0463",
publisher = "Oxford University Press",

}

Jorquera, R, Ortiz, R, Ossandon, F, Cárdenas, JP, Sepúlveda, R, González, C & Holmes, DS 2016, 'SinEx DB: a database for single exon coding sequences in mammalian genomes', Database : the journal of biological databases and curation, vol. 2016. https://doi.org/10.1093/database/baw095

SinEx DB : a database for single exon coding sequences in mammalian genomes. / Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F.; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S.

En: Database : the journal of biological databases and curation, Vol. 2016, 01.01.2016.

Resultado de la investigación: Article

TY - JOUR

T1 - SinEx DB

T2 - a database for single exon coding sequences in mammalian genomes

AU - Jorquera, Roddy

AU - Ortiz, Rodrigo

AU - Ossandon, F.

AU - Cárdenas, Juan Pablo

AU - Sepúlveda, Rene

AU - González, Carolina

AU - Holmes, David S.

PY - 2016/1/1

Y1 - 2016/1/1

N2 - Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.

AB - Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.

UR - http://www.scopus.com/inward/record.url?scp=85017639415&partnerID=8YFLogxK

U2 - 10.1093/database/baw095

DO - 10.1093/database/baw095

M3 - Article

C2 - 27278816

AN - SCOPUS:85017639415

VL - 2016

JO - Database : the journal of biological databases and curation

JF - Database : the journal of biological databases and curation

SN - 1758-0463

ER -