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EMBOSS: showorf |
It uses codon frequency files to do the translation. You can specify the codon frequency file that you use with the '-cfile' option. The default table is 'Ehum.cut'.
% showorf Pretty output of DNA translations Input sequence: embl:paamir Select Frames To Translate 0 : None 1 : F1 2 : F2 3 : F3 4 : R1 5 : R2 6 : R3 Select one or more values [1,2,3,4,5,6]: Output file [paamir.showorf]:
Mandatory qualifiers: [-sequence] sequence Sequence USA -frames list Select one or more values [-outfile] outfile Output file name Optional qualifiers: -[no]ruler bool Add a ruler -[no]plabel bool Number translations -[no]nlabel bool Number DNA sequence Advanced qualifiers: -cfile codon Codon usage file -width integer Width of screen General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required | ||||||||||||||
-frames | Select one or more values |
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1,2,3,4,5,6 | ||||||||||||||
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.showorf | ||||||||||||||
Optional qualifiers | Allowed values | Default | |||||||||||||||
-[no]ruler | Add a ruler | Yes/No | Yes | ||||||||||||||
-[no]plabel | Number translations | Yes/No | Yes | ||||||||||||||
-[no]nlabel | Number DNA sequence | Yes/No | Yes | ||||||||||||||
Advanced qualifiers | Allowed values | Default | |||||||||||||||
-cfile | Codon usage file | Codon usage file in EMBOSS data path | Ehum.cut | ||||||||||||||
-width | Width of screen | Integer 10 or more | 50 |
The true ORFs are 1..109 (amiB partial) 135..1292 (amiC) 1289..1879 (amiR) 1925..end (amiS partial)
SHOWORF of PAAMIR from 1 to 2167 ---------|---------|---------|---------|---------| 1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacggga 50 F1 1 G T A G R A S A R S P P A G R R E 17 F2 1 V P L A E H L L D H H Q P G D G N 17 F3 1 Y R W P S I C S I T T S R A T G 16 ---------|---------|---------|---------|---------| 51 actgcacgatctacctggcgagcctggagcacgagcgggttcgcttcgta 100 F1 18 L H D L P G E P G A R A G S L R T 34 F2 18 C T I Y L A S L E H E R V R F V 33 F3 17 T A R S T W R A W S T S G F A S Y 33 ---------|---------|---------|---------|---------| 101 cggcgctgagcgacagtcacaggagaggaaacggatgggatcgcaccagg 150 F1 35 A L S D S H R R G N G W D R T R 50 F2 34 R R * A T V T G E E T D G I A P G 14 F3 34 G A E R Q S Q E R K R M G S H Q E 50 ...................... ---------|---------|---------|---------|---------| 1851 agttgctgggaaacgagccgtccgcctgagcgatccgggccgaccagaac 1900 F1 341 V A G K R A V R L S D P G R P E Q 357 F2 203 L L G N E P S A * A I R A D Q N 7 F3 5 S C W E T S R P P E R S G P T R T 21 ---------|---------|---------|---------|---------| 1901 aataacaagaggggtatcgtcatcatgctgggactggttctgctgtacgt 1950 F1 1 * Q E G Y R H H A G T G S A V R 15 F2 8 N N K R G I V I M L G L V L L Y V 24 F3 22 I T R G V S S S C W D W F C C T L 38 ---------|---------|---------|---------|---------| 1951 tggcgcggtgctgtttctcaatgccgtctggttgctgggcaagatcagcg 2000 F1 16 W R G A V S Q C R L V A G Q D Q R 32 F2 25 G A V L F L N A V W L L G K I S G 41 F3 39 A R C C F S M P S G C W A R S A 54 ---------|---------|---------|---------|---------| 2001 gtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagcgcctgc 2050 F1 33 S G G G G D Q L P G R R A E R L R 49 F2 42 R E V A V I N F L V G V L S A C 57 F3 55 V G R W R * S T S W S A C * A P A 3 ---------|---------|---------|---------|---------| 2051 gtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100 F1 50 R V L P D L F R S S R A G L A E 65 F2 58 V A F Y L I F S A A A G Q G S L K 74 F3 4 S R S T * S F P Q Q P G R A R * R 1 ---------|---------|---------|---------|---------| 2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccg 2150 F1 66 G R S A D P A I R F Y L S V G G R 82 F2 75 A G A L T L L F A F T Y L W V A A 91 F3 2 P E R * P C Y S L L P I C G W P 12 ---------|------- 2151 ccaaccagttcctcgag 2167 F1 83 Q P V P R 87 F2 92 N Q F L E 96 F3 13 P T S S S 17
The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS' directory of the EMBOSS distribution. If the name of a codon usage file is specified on the command line with the '-cfile' option, then this file will first be searched for in the current directory and then in the 'data/CODONS' directory of the EMBOSS distribution.
To see the available EMBOSS codon usage files, run:
% embossdata -showall
To fetch one of the codon usage tables (for example 'Emus.cut') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Emus.cut
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
coderet | Extract CDS, mRNA and translations from feature tables |
getorf | Finds and extracts open reading frames (ORFs) |
marscan | Finds MAR/SAR sites in nucleic sequences |
plotorf | Plot potential open reading frames |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
showseq | Display a sequence with features, translation etc |
transeq | Translate nucleic acid sequences |
wobble | Wobble base plot |