Recode-2: new design, new search tools, and many more genes

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.

Figure 1.

Entity-Relationship diagram for the Recode-2 database. The database schematic shows the relationships between the database tables. Each Recode-2 entry is composed of one entry in the Recode-2 table and a variable number of entries in related tables. PK (Primary Key) indicates the row selected as the unique identifier for a table. FK (Foreign Key) indicates rows of a table whose values match those in the primary key of a related table. (This ensures the constancy of the database.) The arrows show the connection relationships between the various tables (PK to FK).

Figure 2.

Screenshots from the Recode-2 database for the entry describing +1 frameshifting in human antizyme 1. (A) Annotated sequence of the human antizyme 1 gene. Colouring and formatting of the text highlights functional elements according to a scheme described on the Help page of the Recode-2 database and within the Recode-1 logo. (B) Structure of the stimulatory RNA pseudoknot. (C) The Recode1 logo.