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Introduction


RECODE is a database of the utilization of ribosomal rameshifting, translational bypassing and mRNA specific codon redefinition for gene expression. Frameshifting at a particular site often yields two protein products from one coding sequence and sometimes serves a regulatory purpose by acting as a sensor of the level of product protein or of some external ligand. Bypassing (hopping) allows the coupling of two ORFs separated on an mRNA by a coding gap. Codon redefinition occurs when a stop codon specifies a standard amino acid (often glutamine or tryptophan), or the 21st amino acid selenocysteine. These recoding events are in competition with standard decoding and are site specific. There is a site at which the non-standard decoding event occurs and the efficiency of recoding at this site is elevated by additional stimulatory signals present in the same mRNA or occasionally its protein product.
The sequence of the genes that utilize recoding for their expression are in the database. The recoding sites and the known stimulatory signals are indicated together with notes on factors that are known to influence the events.

How to use this database

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Input

In all fields signs * and ? can be used. * means anything with any length and ? means any sign at this position. 
Organism names
The organism name or part of the name should be typed in order to restrict the search within a particular organism. It is also possible to restrict the search within prokaryotes, archea, eukaryotes or viruses and bacteriophages by marking corresponding squares. 
Gene name
This field contains information only about the gene name, but not about the protein encoded by this gene, i.e. it is better to search for prfB than for RF2 in this field.
Cis-elements
Cis-elements are those signals that influence recoding and are encoded in the gene or messenger RNA. All known cis-elements are present in the scroll-bar menu. There are two fields for the cis-elements, so that a search is possible for more than one cis-element. 
Trans-elements
Many different factors outside of mRNA can influence recoding: small ligands, proteins or tRNAs. 
Product/Function
This field allows a search for the proteins whose synthesized utilizes recoding. A search can be performed using the common name of the protein or words related to their function. 

Output

The short output contains just the name of the organism, gene and type of recoding. This information for each entry is within one row. In order to get detailed information, the corresponding entry should be clicked or alternatively this information can be found at the bottom of the page. The detailed output contains almost all information stored in the database for each entry. Very often the positions of the cis-elemnets are very important and so cis-elements are highlighted in the corresponding DNA sequence.

The following markings are used in this database (the logo at the top of the page can be used as the key to these markings):
Bold – any important sites within the corresponding mRNA, which are known to have effect on recoding.
Underlined – particular sites where recoding takes place.
Italics – peptide signal encoded within the mRNA
Blue – initiation codons (obviously initiation codons do not necessarily play a role in recoding, but their highlighting in the sequence is useful for finding gene starts)
Red – stop codons
Brown – Shine-Dalgarno sequence 
Green and violet – double-stranded RNAs within RNA secondary structure, violet is used in pseudoknots in order to discriminate between two stems.

It is difficult to fit all the available information about recoding in this database. More detailed information is available in the primary research papers. Corresponding references are given for each entry with hyper links to Medline abstracts.