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Virtual Ribosome - version 1.1

The Virtual Ribosome is a comprehensive tool for translating DNA sequences to the corresponding peptide sequences.

Besides being a strong translation tool in it's own right (with an integrated ORF finder, support for all translation tables defined by the NCBI taxonomy group, and a number of options regarding START and STOP codons), the Virtual Ribosome can work directly on files containing annotation of gene structure. This makes it easy to map various aspect of Intron/Exon structure onto the translated sequence.

E.coli ribosome (1PNX / 1PNY)

Instructions Output format Software download Article abstract

Paste in DNA sequences in FASTA, GenBank or TAB format

Upload DNA sequences in FASTA, GenBank or TAB format
View example DNA files

Instructions: Basic usage - Paste in or upload one or more DNA sequences in FASTA (sequence only), GenBank (CDS sections are processed) or TAB (sequence and intron/exon annotation) format and hit submit. The Virtual Ribosome will then translate the DNA sequences using the standard genetic code (by default). Options can be customized in the section below.

Options

Reading frame


Reading frame selection is ignored if Intron/Exon annotation is supplied
[details]

Translation table:


[details]

ORF finder


Scan the reading frame(s) specified above for ORFs
[details]

Start codons

First codon is start codon
All codons are internal
Alternative (non-methionine) start codons will code for methionine if used as a start codon.
[details]

Stop codons

Read through
Terminate
If multiple reading frames are selected (e.g. "all") this option will always be set to "Read through"
[details]

Gene structure annotation

Exon numbering
Intron position and phase
Only for relevant for GenBank and TAB files
[details]

Restrictions:

Please read the CBS access policies for information about limitations on the daily number of submissions. The command-line version of the Virtual Ribosome is free software, and be downloaded here: Software Download.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.

CITATIONS

For publication of results, please cite:

Virtual Ribosome - a comprehensive translation tool with support for sequence feature integration.
Rasmus Wernersson.
Nucl. Acids Res. 2006 34: W385-W388

View the abstract.

PORTABLE VERSION

The commandline version of the Virtual Ribosome is open source software (GPL license) and can be downloaded here.

If you require the Virtual Ribosome on a commerical license, please contact software@cbs.dtu.dk.

GETTING HELP

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This file was last modified Friday 7th 2013f June 2013 11:58:31 GMT