![]() |
EMBOSS: prettyseq |
Slightly unusually, this application uses the codon usage tables to translate the codons.
% prettyseq Input sequence: embl:paamir Range(s) to translate [1-2167]: 135-1292 Output file [paamir.prettyseq]:
Mandatory qualifiers: [-sequence] sequence Sequence USA -range range Range(s) to translate [-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 |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
-range | Range(s) to translate | Sequence range | Whole sequence |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.prettyseq |
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 | 60 |
The format of the range file is:
An example range file is:
# this is my set of ranges 12 23 4 5 this is like 12-23, but smaller 67 10348 interesting region
PRETTYSEQ of PAAMIR from 1 to 2167 ---------|---------|---------|---------|---------|---------| 1 GGTACCGCTGGCCGAGCATCTGCTCGATCACCACCAGCCGGGCGACGGGAACTGCACGAT 60 ---------|---------|---------|---------|---------|---------| 61 CTACCTGGCGAGCCTGGAGCACGAGCGGGTTCGCTTCGTACGGCGCTGAGCGACAGTCAC 120 ---------|---------|---------|---------|---------|---------| 121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180 1 M G S H Q E R P L I G L L F S E 16 ---------|---------|---------|---------|---------|---------| 181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240 17 T G V T A D I E R S H A Y G A L L A V E 36 ---------|---------|---------|---------|---------|---------| 241 agcaactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc 300 37 Q L N R E G G V G G R P I E T L S Q D P 56 ---------|---------|---------|---------|---------|---------| 301 ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccgggggg 360 57 G G D P D R Y R L C A E D F I R N R G V 76 ---------|---------|---------|---------|---------|---------| 361 tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg 420 77 R F L V G C Y M S H T R K A V M P V V E 96 ---------|---------|---------|---------|---------|---------| 421 agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga 480 97 R A D A L L C Y P T P Y E G F E Y S P N 116 ---------|---------|---------|---------|---------|---------| 481 acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga 540 117 I V Y G G P A P N Q N S A P L A A Y L I 136 ---------|---------|---------|---------|---------|---------| 541 ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa 600 137 R H Y G E R V V F I G S D Y I Y P R E S 156 ---------|---------|---------|---------|---------|---------| 601 gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct 660 157 N H V M R H L Y R Q H G G T V L E E I Y 176 ---------|---------|---------|---------|---------|---------| 661 acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg 720 177 I P L Y P S D D D L Q R A V E R I Y Q A 196 ---------|---------|---------|---------|---------|---------| 721 cgcgcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcg 780 197 R A D V V F S T V V G T G T A E L Y R A 216 ---------|---------|---------|---------|---------|---------| 781 ccatcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcg 840 217 I A R R Y G D G R R P P I A S L T T S E 236 ---------|---------|---------|---------|---------|---------| 841 aggcggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgcctt 900 237 A E V A K M E S D V A E G Q V V V A P Y 256 ---------|---------|---------|---------|---------|---------| 901 acttctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttct 960 257 F S S I D T P A S R A F V Q A C H G F F 276 ---------|---------|---------|---------|---------|---------| 961 tcccggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgc 1020 277 P E N A T I T A W A E A A Y W Q T L L L 296 ---------|---------|---------|---------|---------|---------| 1021 tcggccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgt 1080 297 G R A A Q A A G N W R V E D V Q R H L Y 316 ---------|---------|---------|---------|---------|---------| 1081 acgacatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccaca 1140 317 D I D I D A P Q G P V R V E R Q N N H S 336 ---------|---------|---------|---------|---------|---------| 1141 gccgcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggc 1200 337 R L S S R I A E I D A R G V F Q V R W Q 356 ---------|---------|---------|---------|---------|---------| 1201 agtcgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggt 1260 357 S P E P I R P D P Y V V V H N L D D W S 376 ---------|---------|---------|---------|---------|---------| 1261 ccgccagcatgggcgggggaccgctcccatgaGCGCCAACTCGCTGCTCGGCAGCCTGCG 1320 377 A S M G G G P L P * 385 ---------|---------|---------|---------|---------|---------| 1321 CGAGTTGCAGGTGCTGGTCCTCAACCCGCCGGGGGAGGTCAGCGACGCCCTGGTCTTGCA 1380 ...............
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
cusp | Create a codon usage table |
getorf | Finds and extracts open reading frames (ORFs) |
plotorf | Plot potential open reading frames |
remap | Display a sequence with restriction cut sites, translation etc |
showorf | Pretty output of DNA translations |
showseq | Display a sequence with features, translation etc |
transeq | Translate nucleic acid sequences |