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If you need help with the bioinformatics programs, see the "Getting Help" section below the program.
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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. |
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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 can be downloaded on the "Software Download" tab.
Confidentiality:
The sequences are kept confidential and will be deleted
after processing.
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
The commandline version of the Virtual Ribosome is open source software (GPL license) and can be downloaded on the "Software Download" tab.
If you require the Virtual Ribosome on a commerical license, please contact software@cbs.dtu.dk.
Start by pasting in (or uploading) you DNA sequences in FASTA (sequence only), GenBank (CDS elements will be extracted) or TAB (sequence + annotation) format. Free format: if you have a single sequence you want to translate, you can simply paste it in. In this case all non-alphabetic characters (such as numbers) are ignored, making it easy to just copy and paste the sequence from most other data formats.
Hit "Submit query" to run the translation using the Standard Genetic Code and default parameters.
This is the single most important option in the Virtual Ribosome, since it is here it is possible to change the translation table used. All translation tables defined by the NCBI taxonomy group can be selected (see details here: The Genetic Codes [NCBI]). Please notice that the alternative start codons defined in each translation table is also used. For example, in the Standard Genetic Code (see table below), the codons TTG and CTG is allowed as methionie coding start-codons.
Standard Genetic code
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M---------------M---------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
This option is closely related to the alternative start-codons mentioned above. By default the very first codon in the DNA sequence, is considered to be the start-codon which means the special rules of alternative start-codons applies and (for example) the codon TTG will code for methionie and not leucine as when the codon is used internally.
By selecting the "All codons are internal" option all of the sequence is considered internal and start-codon rules are not applied (useful for working with sequence fragments).
This option determines if the tranlation should be terminated at the first encountered stop-codon or not. The default is to read through the entire sequence marking stop-codons with "*".
This option governs the reading frame to use for translation. It's possibe to select either a single reading frame (1, 2, 3 on the plus strand and -1, -2, -3 on the minus strand), or a set of multiple reading frames ("all" = all 6; "plus" = 1, 2, 3; "minus" = -1, -2, -3).
When a single reading frame is selected, the output is (obviously) shown in regard to this frame only. For example:
VIRTUAL RIBOSOME
----------------
Translation table: Standard SGC0
>Seq1
Reading frame: 1
M V L S A A D K G N V K A A W G K V G G H A A E Y G A E A L
5' ATGGTGCTGTCTGCCGCCGACAAGGGCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCGGCCACGCTGCAGAGTATGGCGCAGAGGCCCTG 90
>>>...)))..............................................................................)))
E R M F L S F P T T K T Y F P H F D L S H G S A Q V K G H G
5' GAGAGGATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTCCCCCACTTCGACCTGAGCCACGGCTCCGCGCAGGTCAAGGGCCACGGC 180
......>>>...))).......................................))).................................
A K V A A A L T K A V E H L D D L P G A L S E L S D L H A H
5' GCGAAGGTGGCCGCCGCGCTGACCAAAGCGGTGGAACACCTGGACGACCTGCCCGGTGCCCTGTCTGAACTGAGTGACCTGCACGCTCAC 270
..................)))..................)))......))).........)))......)))......))).........
K L R V D P V N F K L L S H S L L V T L A S H L P S D F T P
5' AAGCTGCGTGTGGACCCGGTCAACTTCAAGCTTCTGAGCCACTCCCTGCTGGTGACCCTGGCCTCCCACCTCCCCAGTGATTTCACCCCC 360
...)))...........................))).........))))))......)))..............................
A V H A S L D K F L A N V S T V L T S K Y R *
5' GCGGTCCACGCCTCCCTGGACAAGTTCTTGGCCAACGTGAGCACCGTGCTGACCTCCAAATACCGTTAA 429
...............))).........)))..................)))...............***
Annotation key:
>>> : START codon (strict) ))) : START codon (alternative) *** : STOP
When multiple reading frames are selected the peptides are "stacked" in the visualization, as seen in the example below. Notice how the START codon "arrows" are reversed on the minus strand to indicate the direction of translation.
VIRTUAL RIBOSOME
----------------
Translation table: Standard SGC0
>Seq1 - reading frame(s): all
G A V C R R Q G Q C Q G R L G Q G W R P R C R V W R R G P
W C C L P P T R A M S R P P G A R L A A T L Q S M A Q R P W
M V L S A A D K G N V K A A W G K V G G H A A E Y G A E A L
5' ATGGTGCTGTCTGCCGCCGACAAGGGCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCGGCCACGCTGCAGAGTATGGCGCAGAGGCCCTG 90
>>>...))).)))...............>>>..........)))........))).........)))......>>>...........)))
....................(((...(((..***(............(((.................(((.........(((........
3' TACCACGACAGACGGCGGCTGTTCCCGTTACAGTTCCGGCGGACCCCGTTCCAACCGCCGGTGCGACGTCTCATACCGCGTCTCCGGGAC 90
H H Q R G G V L A I D L G G P A L N A A V S C L I A C L G Q
T S D A A S L P L T L A A Q P L T P P W A A S Y P A S A R
P A T Q R R C P C H * P R R P C P Q R G R Q L T H R L P G P
Annotation key:
PLUS strand ----------- >>> : START codon (strict) ))) : START codon (alternative) *** : STOP |
MINUS strand ------------ <<< : START codon (strict) ((( : START codon (alternative) *** : STOP |
The Virtual Ribosome has the option of scanning the input DNA sequence for ORFs (Open Reading Frames).
For each sequence the longest ORF is reported. The corresponding DNA fragment is also included for download (embedded in the comment field of the TAB file). For each sequence the specified reading frames are scanned for ORFs. The citeria for opening an ORF can be adjusted as follows:
The advanced options relates the behavior of the translation when TAB format sequences containing annotation of Intron/exon structure has been used as the input (see detail description of TAB files below).
When the Inton/Exon structure is known, the Virtual Ribosom automatically extract the exonic parts of the sequence and performs the translation only on these. Following translation, an analysis of the underlying Intron/Exon structure is performed and used to add annotation to the protein sequence, in the form of a TAB file.
Two types on analysis are available:
1) Exon numbering: Each amino-acid is annotated the the number of the exon which encoded it (or a least hosted the first nucleotide in the codon).
VIRTUAL RIBOSOME ---------------- Translation table: Yeast Mitochondrial SGC2 >Q0045 - translation and annotation of the exonic structure pep: MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVVGHAVLMIFFLVMPALIGGFGNYLLPLMIGA 90 ann: 111111111111111111111111111111111111111111111111111111111222222222222333333333333444444444 90 pep: TDTAFPRINNIAFWVLPMGLVCLVTSTLVESGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH 180 ann: 444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444 180 pep: KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFGHPEVYILIIPGFGIISHVVSTYSKKPVFGE 270 ann: 444444444444444444444444444444444444444444444444444444444444555555555555555555555555555555 270 pep: ISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN 360 ann: 555555555555555555555555555555555555555555555555555555666666666666666666666666666666666666 360 pep: ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIGANVIFFPMHFLGINGMPRRIPDYPDAFAGW 450 ann: 666666666777777777888888888888888888888888888888888888888888888888888888888888888888888888 450 pep: NYVASIGSFIATLSLFLFIYILYDQLVNGLNNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS* 535 ann: 8888888888888888888888888888888888888888888888888888888888888888888888888888888888888 535
TAB files containing exon-number annotation can be used directly in the FeatureMap3D server, for mapping the underlying exon-structure onto protein 3D structures.
2) Intron pos vs. reading frame: The underlying reading frame is determined, and an annotation of intron positions and intron phase is generated.
Phase 0 - an intron exists right before the codon encoding the amino-acid.
Phase 1 - an intron exists in between positions 1 and 2 of the codon.
Phase 2 - an intron exists in between positions 2 and 3 of the codon.
VIRTUAL RIBOSOME ---------------- Translation table: Yeast Mitochondrial SGC2 >Q0045 - translation and annotation of the position and phase of the introns pep: MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVVGHAVLMIFFLVMPALIGGFGNYLLPLMIGA 90 ann: ........................................................1...........1............0........ 90 pep: TDTAFPRINNIAFWVLPMGLVCLVTSTLVESGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH 180 ann: .......................................................................................... 180 pep: KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFGHPEVYILIIPGFGIISHVVSTYSKKPVFGE 270 ann: ............................................................0............................. 270 pep: ISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN 360 ann: ......................................................0................................... 360 pep: ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIGANVIFFPMHFLGINGMPRRIPDYPDAFAGW 450 ann: .........0.......1........................................................................ 450 pep: NYVASIGSFIATLSLFLFIYILYDQLVNGLNNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS* 535 ann: ..................................................................................... 535
The idea is simply to have a string in addtion to the DNA/peptide sequence which describes the properties of the sequence. This is done using a simple one-letter code. All this is described in great details for DNA sequences on the FeatureExtract server and the publication describing the server [FeatureExtract - extraction of sequence annotation made easy, Wernersson, 2005]. Here it is best illustrated by an example:
Sequence: ATGTCTACATATGAAGGTATGTAA Annotation: (EEEEEEEEEEEEEE)DIIIIIII E: Exon I: Intron (: Start of exon ): End of exon D: Donor site A: Accepter site
The Virtual Ribosome looks for the regions annotated as (EEEEEE{many E's}EEEEE) for finding the exoninc part of a sequence.
The TAB for is very simple. Each line hold the information of exactly one sequence in four field separated by the TAB character:
Name Seq Ann ComName : Name of the sequence.
TAB format files containing information about the Intron/Exon structure, can be generated from GenBank files using the FeatureExtract server.
The Virtual Ribosome has the option of working directly with GenBank files. When a GenBank file is supplied, all CDS elements is extracted to a TAB file (see above) containing Intron/Exon annotation prior to the translation. This is done by processing the GenBank entry with the FeatureExtract software using default parameters.
For greated control of the GenBank parsing process, please use the FeatureExtract server directly and submit the resultant TAB files to the Virtual Ribosome.
>AB001981_alpha-A_Pigeon ATGGTGCTGTCTGCCAACGACAAGAGCAACGTGAAGGCCGTCTTCGGCAAAATCGGCGGC CAGGCCGGTGACTTGGGTGGTGAAGCCCTGGAGAGGTTGTTCATCACCTACCCCCAGACC AAGACCTACTTCCCCCACTTCGACCTGTCACATGGCTCCGCTCAGATCAAGGGGCACGGC AAGAAGGTGGCGGAGGCACTGGTTGAGGCTGCCAACCACATCGATGACATCGCTGGTGCC CTCTCCAAGCTGAGCGACCTCCACGCCCAAAAGCTCCGTGTGGACCCCGTCAACTTCAAA CTGCTGGGTCACTGCTTCCTGGTGGTCGTGGCCGTCCACTTCCCCTCTCTCCTGACCCCG GAGGTCCATGCTTCCCTGGACAAGTTCGTGTGTGCCGTGGGCACCGTCCTTACTGCCAAG TACCGTTAA >J00043_Alpha-i_Goat ATGGTGCTGTCTGCCGCCGACAAGTCCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCGGC AACGCTGGAGCTTATGGCGCAGAGGCTCTGGAGAGGATGTTCCTGAGCTTCCCCACCACC AAGACCTACTTCCCCCACTTCGACCTGAGCCACGGCTCGGCCCAGGTCAAGGGCCACGGC GAGAAGGTGGCCGCCGCGCTGACCAAAGCGGTGGGCCACCTGGACGACCTGCCCGGTACT CTGTCTGATCTGAGTGACCTGCACGCCCACAAGCTGCGTGTGGACCCGGTCAACTTTAAG CTTCTGAGCCACTCCCTGCTGGTGACCCTGGCCTGCCACCTCCCCAATGATTTCACCCCC GCGGTCCACGCCTCCCTGGACAAGTTCTTGGCCAACGTGAGCACCGTGCTGACCTCCAAA TACCGTTAA >AF098919_Embryonic_Alpha-pi_Chicken ATGGCACTGACCCAAGCTGAGAAGGCTGCCGTGACCACCATCTGGGCAAAGGTGGCTACC CAGATTGAGTCCATTGGGCTGGAATCACTGGAGAGGCTTTTTGCCAGCTATCCTCAGACG AAAACCTACTTCCCTCACTTTGATGTCAGCCAAGGCTCAGTTCAGCTTCGTGGTCACGGC TCCAAGGTCCTGAATGCCATTGGGGAAGCTGTGAAGAACATCGATGACATTAGAGGTGCT TTGGCCAAACTCAGCGAGCTGCATGCTTACATCCTCAGGGTGGACCCAGTGAACTTCAAG CTGCTTTCCCACTGTATCCTGTGCTCTGTGGCTGCCCGCTATCCCAGTGATTTCACCCCA GAAGTTCATGCTGCGTGGGACAAGTTCCTGTCCAGCATTTCCTCTGTTCTGACTGAGAAA TACAGATAAThe Example above can be pasted directly into the text-field in the main windows of the Virtual Ribosome.
Here is a file with 11 Alpha-globins in FASTA format: alpha-globins.fsa.
LOCUS GOTHBAII 1691 bp DNA linear MAM 27-APR-1993
DEFINITION Goat adult alpha-ii-globin gene, complete sequence.
ACCESSION J00044
VERSION J00044.1 GI:164125
KEYWORDS alpha-globin; globin.
SOURCE Capra hircus (goat)
ORGANISM Capra hircus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;
Pecora; Bovidae; Caprinae; Capra.
REFERENCE 1 (bases 1 to 1691)
AUTHORS Schon,E.A., Wernke,S.M. and Lingrel,J.B.
TITLE Gene conversion of two functional goat alpha-globin genes preserves
only minimal flanking sequences
JOURNAL J. Biol. Chem. 257 (12), 6825-6835 (1982)
PUBMED 6282825
FEATURES Location/Qualifiers
source 1..1691
/organism="Capra hircus"
/mol_type="genomic DNA"
/db_xref="taxon:9925"
CDS join(745..839,941..1145,1250..1378)
/note="alpha-ii globin"
/codon_start=1
/protein_id="AAA30910.1"
/db_xref="GI:164126"
/translation="MVLSAADKSNVKAAWGKVGSNAGAYGAEALERMFLSFPTTKTYF
PHFDLSHGSAQVKGHGEKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLL
SHSLLVTLACHHPSDFTPAVHASLDKFLANVSTVLTSKYR"
exon <745..839
/note="alpha-ii globin"
exon 941..1145
exon 1250..>1378
/note="alpha-ii globin"
ORIGIN
1 ctgcaggaac cagcacctgg gagaagagac ttgaacccgg acttgaactc cttgcaaatt
61 gctgtaaccc gctctcagta tctgttcctt ccaagactgc cactcagttg cacccaaaaa
121 ctctctgcgg aaagaaagga agctcgaagc gccaaggctg aagaggaaca ggagggttgg
181 acgggggtgg ggaggaattc gcgattacat gtgaacggtg agccaagtgt gttgcgtcgg
241 gctgcctctg gcatggacta ggcgcactca gtcgcccgtt ccttcactga tactgcccaa
301 gtttaaaatg cccagagtgt gccaagctta ggtccggggt gggtagacgg gctgacttac
361 tcccttccgt tctcaagaca gctggggaac tcctgcagga tgcaggagcg ggcatctacc
421 cagctccaca atcccgcccc tgccacctgg cgcgaggcta ccacgtccgg ggaaggtgga
481 cgcagcgggc gggaagcaga cggtggaagc aagaaccccc ggtcagagtc caggtctggg
541 tgggtgaggg aagcacccat cgcccggccg ggcgcaggtc ggactccgcg cgccccctgc
601 ggtcctggtc cggccgcgca tgccgcgtgc cagccaatga gcgcagcgcg ggcgggcgtg
661 cacctggagc cgggcgcata aaggctcgcg cactcgcagc cccgcactct tctggttctg
721 acccagactc agagagaatc caccatggtg ctgtctgccg ccgacaagtc caatgtcaag
781 gccgcctggg gcaaggttgg cagcaacgct ggagcttatg gcgcagaggc tctggagagg
841 tgagcaccgc acccgccccg aggggaccgg gccgctcgcc gggcgcgtcc ttgtaccggg
901 cctctcggcc tgagcccggc tttcccgcct cttcacccag gatgttcctg agcttcccca
961 ccaccaagac ctacttcccc cacttcgacc tgagccacgg ctcggcccag gtcaagggcc
1021 acggcgagaa ggtggccgcc gcgctgacca aagcggtggg ccacctggac gacctgcccg
1081 gtactctgtc tgatctgagt gacctgcacg cccacaagct gcgtgtggac ccggtcaact
1141 ttaaggtgag ctcgcgggcc gggccgggac agacctgggc tagcggggca gagaatgccg
1201 cggcggcccc acccagcccc cgccccactg acgtcccctc tctcggcagc ttctgagcca
1261 ctccctgctg gtgaccctgg cctgccacca ccccagtgat ttcacccccg cggtccacgc
1321 ctccctggac aagttcttgg ccaacgtgag caccgtgctg acctccaaat accgttaagc
1381 tggagcctcg gccaccccta ccctggcctg gagcgccctt gcgctctgcg cactctcacc
1441 tcctgatctt tgaataaagt ctgagtgggc tgcagtgtct gtctgtagcc tcgggtctct
1501 gtgtccgcga accggcccag gttctcattg cctcggacca aggagctctc aggcagctag
1561 agagagaagg ggaaaactgg acggaggggt gggggtgcag cctgccccac tgccactacc
1621 tgggattctc tgggcagccc tcaccctcag cctggagtga tttctgagta tcttggccct
1681 tccctgaatt c
//
Here is a file with 11 Alpha-globins (9 GenBank entries) in a multi-GenBank file: alpha-globins.gbk.
Here is a file with 11 Alpha-globins in TAB format: alpha-globins.tab. The file contains both DNA sequence and annotation of the Intron/Exon structure. It was generated by parsing the GenBank entries listed below using the FeatureExtract server. In this file the naming of each entry has been selected to indicate both the type of alpha-globin and the organism.
AB001981 X01831 J00923 J00043 J00044 X01086 X07053 AF098919
An reformatted human-readable view of the first entry in the TAB file looks like this:
Name: 'AB001981_alpha-D_Pigeon' ATGCTGACCGACTCTGACAAGAAGCTGGTCCTGCAGGTGTGGGAGAAGGTGATCCGCCAC 59 (EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 59 CCAGACTGTGGAGCCGAGGCCCTGGAGAGGTGCGGGCTGAGCTTGGGGAAACCATGGGCA 119 EEEEEEEEEEEEEEEEEEEEEEEEEEEE)DIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 119 AGGGGGGCGACTGGGTGGGAGCCCTACAGGGCTGCTGGGGGTTGTTCGGCTGGGGGTCAG 179 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 179 CACTGACCATCCCGCTCCCGCAGCTGTTCACCACCTACCCCCAGACCAAGACCTACTTCC 239 IIIIIIIIIIIIIIIIIIIIIA(EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 239 CCCACTTCGACTTGCACCATGGCTCCGACCAGGTCCGCAACCACGGCAAGAAGGTGTTGG 299 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 299 CCGCCTTGGGCAACGCTGTCAAGAGCCTGGGCAACCTCAGCCAAGCCCTGTCTGACCTCA 359 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 359 GCGACCTGCATGCCTACAACCTGCGTGTCGACCCTGTCAACTTCAAGGCAGGCGGGGGAC 419 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE)DIIIIIIIIIIII 419 GGGGGTCAGGGGCCGGGGAGTTGGGGGCCAGGGACCTGGTTGGGGATCCGGGGCCATGCC 479 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 479 GGCGGTACTGAGCCCTGTTTTGCCTTGCAGCTGCTGGCGCAGTGCTTCCACGTGGTGCTG 539 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIA(EEEEEEEEEEEEEEEEEEEEEEEEEEEEE 539 GCCACACACCTGGGCAACGACTACACCCCGGAGGCACATGCTGCCTTCGACAAGTTCCTG 599 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 599 TCGGCTGTGTGCACCGTGCTGGCCGAGAAGTACAGATAA 638 EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE) 638 //
Notice: the sequence above CANNOT be paste into the Virtual Ribosome, since it's NOT in TAB format and only serves the purpose of illustrating the content of a TAB file.
Since the command-line programs behind both the FeatureExtract server and the Virtual Ribosome are available as Open-Source packages for download, they can be combined to form a strong tool-chain, as the following example describe.
gb2tab : The program behind the FeatureExtract server. dna2pep : The program behind the Virtual Ribosome server.
All files for the Yeast genome has been download in GenBank format:
genome[raz]:/home/people/raz/projects/genomes/YeastGenomeNov2005> ll *gbf
-rw------- 1 raz user 479K Nov 30 13:59 chr01.gbf
-rw------- 1 raz user 1.8M Nov 30 13:59 chr02.gbf
-rw------- 1 raz user 701K Nov 30 13:59 chr03.gbf
-rw------- 1 raz user 3.3M Nov 30 13:59 chr04.gbf
-rw------- 1 raz user 1.2M Nov 30 13:59 chr05.gbf
-rw------- 1 raz user 592K Nov 30 13:59 chr06.gbf
-rw------- 1 raz user 2.3M Nov 30 13:59 chr07.gbf
-rw------- 1 raz user 1.2M Nov 30 13:59 chr08.gbf
-rw------- 1 raz user 948K Nov 30 13:59 chr09.gbf
-rw------- 1 raz user 1.6M Nov 30 13:59 chr10.gbf
-rw------- 1 raz user 1.4M Nov 30 13:59 chr11.gbf
-rw------- 1 raz user 2.3M Nov 30 13:59 chr12.gbf
-rw------- 1 raz user 2.0M Nov 30 13:59 chr13.gbf
-rw------- 1 raz user 1.7M Nov 30 13:59 chr14.gbf
-rw------- 1 raz user 2.3M Nov 30 13:59 chr15.gbf
-rw------- 1 raz user 2.0M Nov 30 13:59 chr16.gbf
-rw------- 1 raz user 160K Nov 30 13:59 chrmt.gbf
Extract and translate the nuclear genes:
gb2tab chr{0,1}*gbf | dna2pep > yeast_nuc.tab
Extract and translate the mitochondrial genes:
gb2tab chrmt.gbf | dna2pep -m 3 > yeast_mit.tab
Count number of lines = number of genes:
genome[raz]:/home/people/raz/projects/genomes/YeastGenomeNov2005> wc -l yeast_*.tab
19 yeast_mit.tab
5854 yeast_nuc.tab
5873 total
Find the mitochondrial proteins that originates from genes without introns:
genome[raz]:/home/people/raz/projects/genomes/YeastGenomeNov2005> egrep -v "2222+" yeast_mit.tab | cut -f 1
AI1
AAP1
ATP6
OLI1
VAR1
SCEI
COX2
COX3
Follooing translation Virtual Ribosome produces a visualization of DNA, peptide, START and STOP codon, position of transcript and offers the translated sequences in FASTA and TAB format.
Please refer to the "Instructions" tab for a detailed description of the visualization.
>GOTHBAII_745 MVLSAADKSNVKAAWGKVGSNAGAYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG EKVAAALTKAVGHLDDLPGTLSDLSDLHAHKLRVDPVNFKLLSHSLLVTLACHHPSDFTP AVHASLDKFLANVSTVLTSKYR*
The Virtual Ribosome is a DNA translation tool with two areas of focus 1) Providing a strong translation tool in it own right, with an integrated ORF finder, full support for the IUPAC degenerate DNA alphabet and all translation tables defined by the NCBI taxonomy group, including the use of alternative start codons. 2) Integration of sequences feature annotation - in particular native support for working with files containing Intron/Exon structure annotation.
Rasmus Wernersson.
Virtual Ribosome - a comprehensive DNA translation tool with
support for integration of sequence feature annotation
Nucl. Acids Res. 2006 34: W385-W388
Contact
Rasmus Wernersson: raz@cbs.dtu.dk
(Web)
If you need help regarding technical issues (e.g. errors or missing results) contact Technical Support. Please include the name of the service and version (e.g. NetPhos-4.0) and the options you have selected. If the error occurs after the job has started running, please include the JOB ID (the long code that you see while the job is running).
If you have scientific questions (e.g. how the method works or how to interpret results), contact Correspondence.
Correspondence:
Technical Support: