Recode


19783826	Recode-2: new design, new search tools, and many more genes. [PMID: 19783826] Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV. Abstract 'Recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression--a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie. Nucleic Acids Res. 2010:38(Database issue) \| 34 Citations (from Europe PMC, 2025-03-22)
12519954	RECODE 2003. [PMID: 12519954] Baranov PV, Gurvich OL, Hammer AW, Gesteland RF, Atkins JF. Abstract The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information. The Database is freely available at http://recode.genetics.utah.edu/. Nucleic Acids Res. 2003:31(1) \| 43 Citations (from Europe PMC, 2025-03-22)
11125107	RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression. [PMID: 11125107] Baranov PV, Gurvich OL, Fayet O, Prère MF, Miller WA, Gesteland RF, Atkins JF, Giddings MC. Abstract The RECODE database is a compilation of 'programmed' translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding. The database is freely available at http://recode.genetics. utah.edu/. Nucleic Acids Res. 2001:29(1) \| 37 Citations (from Europe PMC, 2025-03-22)

Recode-2: new design, new search tools, and many more genes. [PMID: 19783826]

Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV.

'Recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression--a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie.

Nucleic Acids Res. 2010:38(Database issue) | 34 Citations (from Europe PMC, 2025-03-22)

RECODE 2003. [PMID: 12519954]

Baranov PV, Gurvich OL, Hammer AW, Gesteland RF, Atkins JF.

Abstract

The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information. The Database is freely available at http://recode.genetics.utah.edu/.

Nucleic Acids Res. 2003:31(1) | 43 Citations (from Europe PMC, 2025-03-22)

RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression. [PMID: 11125107]

Baranov PV, Gurvich OL, Fayet O, Prère MF, Miller WA, Gesteland RF, Atkins JF, Giddings MC.

Abstract

The RECODE database is a compilation of 'programmed' translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, trans-factors and cis-elements that influence recoding. The database is freely available at http://recode.genetics. utah.edu/.

Nucleic Acids Res. 2001:29(1) | 37 Citations (from Europe PMC, 2025-03-22)

URL:	http://recode.ucc.ie
Full name:
Description:	Database of translational recoding events
Year founded:	2001
Last update:	2010-04-01
Version:	v2.0
Accessibility:	Accessible
Country/Region:	Ireland

Data type:	DNA RNA
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Expression Literature
Major species:	Homo sapiens
Keywords:	translational recoding event translational search Codon redefinition Ribosome shifts frame

University/Institution:	University College Cork
Address:
City:	Cork
Province/State:
Country/Region:	Ireland
Contact name (PI/Team):	Pavel V. Baranov
Contact email (PI/Helpdesk):	p.baranov@ucc.ie

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Database Commons a catalog of worldwide biological databases