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prettyseq |
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prettyseq reads a nucleotide sequence and writes an output file containing in a clean format the sequence with the translation (within specified ranges) displayed beneath it. The translated nucleic acid region is given lower-case letters with the rest of the input sequence left in the input case. A specified codon usage table is used to translate the codons.
% prettyseq Write a nucleotide sequence and its translation to file Input nucleotide sequence: tembl:x13776 Range(s) to translate [1-2167]: 135-1292 Output file [x13776.prettyseq]: |
Go to the input files for this example
Go to the output files for this example
Write a nucleotide sequence and its translation to file
Version: EMBOSS:6.3.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-range range [Whole sequence] Range(s) to translate
[-outfile] outfile [*.prettyseq] Output file name
Additional (Optional) qualifiers:
-table menu [0] Genetic code to use (Values: 0
(Standard); 1 (Standard (with alternative
initiation codons)); 2 (Vertebrate
Mitochondrial); 3 (Yeast Mitochondrial); 4
(Mold, Protozoan, Coelenterate Mitochondrial
and Mycoplasma/Spiroplasma); 5
(Invertebrate Mitochondrial); 6 (Ciliate
Macronuclear and Dasycladacean); 9
(Echinoderm Mitochondrial); 10 (Euplotid
Nuclear); 11 (Bacterial); 12 (Alternative
Yeast Nuclear); 13 (Ascidian Mitochondrial);
14 (Flatworm Mitochondrial); 15
(Blepharisma Macronuclear); 16
(Chlorophycean Mitochondrial); 21 (Trematode
Mitochondrial); 22 (Scenedesmus obliquus);
23 (Thraustochytrium Mitochondrial))
-[no]ruler boolean [Y] Add a ruler
-[no]plabel boolean [Y] Number translations
-[no]nlabel boolean [Y] Number DNA sequence
Advanced (Unprompted) qualifiers:
-width integer [60] Width of screen (Integer 10 or more)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
od>Any string |
||||
| -osdbname6 -osdbname_restoutseq |
string | Database name to add | Any string | |
| -ossingle6 -ossingle_restoutseq |
boolean | Separate file for each entry | Boolean value Yes/No | N |
| -oufo6 -oufo_restoutseq |
string | UFO features | Any string | |
| -offormat6 -offormat_restoutseq |
string | Features format | Any string | |
| -ofname6 -ofname_restoutseq |
string | Features file name | Any string | |
| -ofdirectory6 -ofdirectory_restoutseq |
string | Output directory | Any string | |
| General qualifiers | ||||
|---|---|---|---|---|
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
ID X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
XX
AC X03487;
XX
DT 02-JUL-1986 (Rel. 09, Created)
DT 24-AUG-2005 (Rel. 84, Last updated, Version 3)
XX
DE Human apoferritin H gene exon 1
XX
KW ferritin.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-512
RX DOI; 10.1093/nar/14.2.721.
RX PUBMED; 3003694.
RA Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
RA Delius H., Cortese R.;
RT "Structure of gene and pseudogenes of human apoferritin H";
RL Nucleic Acids Res. 14(2):721-736(1986).
XX
DR EPD; EP11112; HS_FTH1.
DR RFAM; RF00037; IRE.
XX
FH Key Location/Qualifiers
FH
FT source 1..512
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:9606"
FT misc_feature 65..70
FT /note="GGGCGG box"
FT misc_feature 103..108
FT /note="GGGCGG box"
FT misc_feature 126..131
FT /note="GGGCGG box"
FT promoter 150..154
FT /note="put. TATA box"
FT mRNA 179..500
FT /note="exon 1"
FT CDS join(387..500,X03488.1:50..196,X03488.1:453..578,
FT X03488.1:674..838)
FT /product="apoferritin H subunit"
FT /db_xref="GDB:120617"
FT /db_xref="GOA:P02794"
FT /db_xref="HGNC:3976"
FT /db_xref="InterPro:IPR001519"
FT /db_xref="InterPro:IPR008331"
FT /db_xref="InterPro:IPR009040"
FT /db_xref="InterPro:IPR009078"
FT /db_xref="InterPro:IPR012347"
FT /db_xref="InterPro:IPR014034"
FT /db_xref="PDB:1FHA"
FT /db_xref="PDB:2CEI"
FT /db_xref="PDB:2CHI"
FT /db_xref="PDB:2CIH"
FT /db_xref="PDB:2CLU"
FT /db_xref="PDB:2CN6"
FT /db_xref="PDB:2CN7"
FT /db_xref="PDB:2FHA"
FT /db_xref="PDB:2IU2"
FT /db_xref="PDB:2Z6M"
FT /db_xref="PDB:3ERZ"
FT /db_xref="PDB:3ES3"
FT /db_xref="UniProtKB/Swiss-Prot:P02794"
FT /protein_id="CAA27205.1"
FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
FT SGLAEYLFDKHTLGDSDNES"
FT intron 501..>512
FT /note="intron I"
XX
SQ Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca 60
gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 120
ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 180
gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 240
gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 300
caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 360
gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 420
actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 480
cctacgttta cctgtccatg gtgagcgcgg gc 512
//
|
ID X03487; SV 1; linear; genomic DNA; STD; HUM; 512 BP.
XX
AC X03487;
XX
DT 02-JUL-1986 (Rel. 09, Created)
DT 24-AUG-2005 (Rel. 84, Last updated, Version 3)
XX
DE Human apoferritin H gene exon 1
XX
KW ferritin.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
XX
RN [1]
RP 1-512
RX DOI; 10.1093/nar/14.2.721.
RX PUBMED; 3003694.
RA Costanzo F., Colombo M., Staempfli S., Santoro C., Marone M., Frank R.,
RA Delius H., Cortese R.;
RT "Structure of gene and pseudogenes of human apoferritin H";
RL Nucleic Acids Res. 14(2):721-736(1986).
XX
DR EPD; EP11112; HS_FTH1.
DR RFAM; RF00037; IRE.
XX
FH Key Location/Qualifiers
FH
FT source 1..512
FT /organism="Homo sapiens"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:9606"
FT misc_feature 65..70
FT /note="GGGCGG box"
FT misc_feature 103..108
FT /note="GGGCGG box"
FT misc_feature 126..131
FT /note="GGGCGG box"
FT promoter 150..154
FT /note="put. TATA box"
FT mRNA 179..500
FT /note="exon 1"
FT CDS join(387..500,X03488.1:50..196,X03488.1:453..578,
FT X03488.1:674..838)
FT /product="apoferritin H subunit"
FT /db_xref="GDB:120617"
FT /db_xref="GOA:P02794"
FT /db_xref="HGNC:3976"
FT /db_xref="InterPro:IPR001519"
FT /db_xref="InterPro:IPR008331"
FT /db_xref="InterPro:IPR009040"
FT /db_xref="InterPro:IPR009078"
FT /db_xref="InterPro:IPR012347"
FT /db_xref="InterPro:IPR014034"
FT /db_xref="PDB:1FHA"
FT /db_xref="PDB:2CEI"
FT /db_xref="PDB:2CHI"
FT /db_xref="PDB:2CIH"
FT /db_xref="PDB:2CLU"
FT /db_xref="PDB:2CN6"
FT /db_xref="PDB:2CN7"
FT /db_xref="PDB:2FHA"
FT /db_xref="PDB:2IU2"
FT /db_xref="PDB:2Z6M"
FT /db_xref="PDB:3ERZ"
FT /db_xref="PDB:3ES3"
FT /db_xref="UniProtKB/Swiss-Prot:P02794"
FT /protein_id="CAA27205.1"
FT /translation="MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRD
FT DVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECA
FT LHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPE
FT SGLAEYLFDKHTLGDSDNES"
FT intron 501..>512
FT /note="intron I"
XX
SQ Sequence 512 BP; 80 A; 212 C; 152 G; 64 T; 4 other;
agnncaaacc tnagctccgc cagagcgcgc gaggcctcca gcggccgccc ctcccccaca 60
gcaggggcgg ggntcccgcg cccaccggaa ggagcgggct cggggcgggc ggcgctgatt 120
ggccggggcg ggcctgacgc cgacgcggct ataagagacc acaagcgacc cgcagggcca 180
gacgttcttc gccgagagtc gtcggggttt cctgcttcaa cagtgcttgg acggaacccg 240
gcgctcgttc cccaccccgg ccggccgccc atagccagcc ctccgtcgac ctcttcaccg 300
caccctcgga ctgccccaag gcccccgccg ccgctccagc gccgcgcagc caccgccgcc 360
gccgccgcct ctccttagtc gccgccatga cgaccgcgtc cacctcgcag gtgcgccaga 420
actaccacca ggactcagag gccgccatca accgccagat caacctggag ctctacgcct 480
cctacgttta cctgtccatg gtgagcgcgg gc 512
//
|
One or more of CDS, mRNA, translation can be excluded from the output by using the appropriate qualifiers to the program (i.e. -nocds, etc.)
The ID names of the output sequences are constructed from the name of the input sequence, the type of feature being output (i.e. cds, mrna, pro) and a unique ordinal number for this type to distinguish it from others in this sequence. The name, type and number of separated by underscore characters. Thus the second CDS feature in the sequence 'A12345' would be named 'A12345_cds_2'.
The translations are not made from the coding sequence, they are extracted directly from the translation sequence held in the feature table.
>x03487_cds_1 atgacgaccgcgtccacctcgcaggtgcgccagaactaccaccaggactcagaggccgcc atcaaccgccagatcaacctggagctctacgcctcctacgtttacctgtccatgtcttac tactttgaccgcgatgatgtggctttgaagaactttgccaaatactttcttcaccaatct catgaggagagggaacatgctgagaaactgatgaagctgcagaaccaacgaggtggccga atcttccttcaggatatcaagaaaccagactgtgatgactgggagagcgggctgaatgca atggagtgtgcattacatttggaaaaaaatgtgaatcagtcactactggaactgcacaaa ctggccactgacaaaaatgacccccatttgtgtgacttcattgagacacattacctgaat gagcaggtgaaagccatcaaagaattgggtgaccacgtgaccaacttgcgcaagatggga gcgcccgaatctggcttggcggaatatctctttgacaagcacaccctgggagacagtgat aatgaaagctaa |
>x03487_mrna_1 cagacgttcttcgccgagagtcgtcggggtttcctgcttcaacagtgcttggacggaacc cggcgctcgttccccaccccggccggccgcccatagccagccctccgtcgacctcttcac cgcaccctcggactgccccaaggcccccgccgccgctccagcgccgcgcagccaccgccg ccgccgccgcctctccttagtcgccgccatgacgaccgcgtccacctcgcaggtgcgcca gaactaccaccaggactcagaggccgccatcaaccgccagatcaacctggagctctacgc ctcctacgtttacctgtccatg |
>x03487_pro_1 MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHK LATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSD NES |
>x03487_noncoding_1 agnncaaacctnagctccgccagagcgcgcgaggcctccagcggccgcccctcccccaca gcaggggcggggntcccgcgcccaccggaaggagcgggctcggggcgggcggcgctgatt ggccggggcgggcctgacgccgacgcggctataagagaccacaagcgacccgcagggc >x03487_noncoding_501 gtgagcgcgggc |
CDS mRNA non-c Trans Total Sequence
===== ===== ===== ===== ===== ========
1 1 6 1 8 X03487
|
mRNA Total Sequence
===== ===== ========
1 1 X03487
|
One or more of CDS, mRNA, translation or non-coding regions can be excluded from output with the appropriate qualifiers; "no" is prepended to the qualifier name, for example -nocds would exclude the coding sequence.
The translations are not made from the coding sequence, they are extracted directly from the translation sequence held in the feature table.
The regions of the feature table that concern us are shown below.
This specifies that the coding sequence for the gene is constructed by joining several sections of code, many of which are in other entries in this database:
FT CDS join(U21925.1:818..987,U21926.1:258..420, FT U21927.1:428..520,U21928.1:196..336,U21929.1:279..415, FT U21930.1:895..1014,516..708)
This specifies that the messenger RNA sequence for the gene is constructed by joining several sections of code, many of which are in other entries in this database.
FT mRNA join(M88628.1:1006..1318,M88629.1:221..342, FT M88630.1:101..223,M88631.1:46..258,M88632.1:104..172, FT M88633.1:387..503,M88634.1:51..272,M88635.1:303..564, FT M88635.1:849..1020,M88636.1:282..375,M88637.1:39..253, FT M88638.1:91..241,M88639.1:168..377,M88640.1:627..3732, FT M88641.1:158..311,M88642.1:1051..1263,M88642.1:1550..1778, FT M88642.1:1986..2168,M88642.1:3904..4020, FT M88642.1:4627..4698,M88643.1:39..124,M88644.1:42..197, FT M88645.1:542..686,M88646.1:75..223,M88647.1:109..285, FT 253..2211)
This specifies that the translation of the coding region is as follows:
FT /translation="MAQDSVDLSCDYQFWMQKLSVWDQASTLETQQDTCLHVAQFQEFL FT RKMYEALKEMDSNTVIERFPTIGQLLAKACWNPFILAYDESQKILIWCLCCLINKEPQN FT SGQSKLNSWIQGVLSHILSALRFDKEVALFTQGLGYAPIDYYPGLLKNMVLSLASELRE FT NHLNGFNTQRRMAPERVASLSRVCVPLITLTDVDPLVEALLICHGREPQEILQPEFFEA FT VNEAILLKKISLPMSAVVCLWLRHLPSLEKAMLHLFEKLISSERNCLRRIECFIKDSSL FT PQAACHPAIFRVDEMFRCALLETDGALEIIATIQVFTQCFVEALEKASKQLRFALKTYF FT PYTSPSLAMVLLQDPQDIPRGHWLQTLKHISELLREAVEDQTHGSCGGPFESWFLFIHF FT GGWAEMVAEQLLMSAAEPPTALLWLLAFYYGPRDGRQQRAQTMVQVKAVLGHLLAMSRS FT SSLSAQDLQTVAGQGTDTDLRAPAQQLIRHLLLNFLLWAPGGHTIAWDVITLMAHTAEI FT THEIIGFLDQTLYRWNRLGIESPRSEKLARELLKELRTQV"
| Program name | Description |
|---|---|
| backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
| backtranseq | Back-translate a protein sequence to a nucleotide sequence |
| extractfeat | Extract features from sequence(s) |
| maskfeat | Write a sequence with masked features |
| plotorf | Plot potential open reading frames in a nucleotide sequence |
| prettyseq | Write a nucleotide sequence and its translation to file |
| remap | Display restriction enzyme binding sites in a nucleotide sequence |
| showfeat | Display features of a sequence in pretty format |
| showorf | Display a nucleotide sequence and translation in pretty format |
| showseq | Displays sequences with features in pretty format |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| transeq | Translate nucleic acid sequences |
| twofeat | Finds neighbouring pairs of features in sequence(s) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.