Tehdyt toimenpiteet
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sixpack |
Wiki
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Function
Display a DNA sequence with 6-frame translation and ORFsDescription
sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the three forward and (optionally) three reverse translations in a pretty display format. A genetic code may be specified for the translation. There are various options to control the appearance of the output file. It also writes a file of protein sequences corresponding to any open reading frames that are larger than the specified minimum size: the default of 1 base shows all possible open reading frames.
Algorithm
The program takes the following steps:
The nucleic acid sequence is read in. The required genetic code is read in from the EGC* data files. The three forward and three reverse translations are created. The name and description are written to the output display file. Any required regions to be changed to upper case are changed. Any required regions to be highlighted in HTML colour tags are changed. The reverse sense sequence is placed below the forward sequence. The forward translations are placed above the sequences. The reverse translation are placed below the sequences. The display is written out, split at the ends of lines. Any ORFs that are longer than the specified minimum size are written to the output sequence file.
Usage
Here is a sample session with sixpack
% sixpack Display a DNA sequence with 6-frame translation and ORFs Input nucleotide sequence: tembl:x13776 Output file [x13776.sixpack]: protein output sequence(s) [x13776.fasta]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Display a DNA sequence with 6-frame translation and ORFs
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-outfile] outfile [*.sixpack] Output file name
-outseq seqoutall [
|
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||||||
| [-sequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.sixpack | ||||||||||||||||||||||||||||||||||||
| -outseq | seqoutall | ORF sequence output | Writeable sequence(s) | <*>.format | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -table | list | Genetics code used for the translation |
|
0 | ||||||||||||||||||||||||||||||||||||
| -[no]firstorf | boolean | Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]lastorf | boolean | Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -mstart | boolean | Displays only ORFs starting with an M. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -[no]reverse | boolean | Display also the translation of the DNA sequence in the 3 reverse frames | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -orfminsize | integer | Minimum size of Open Reading Frames (ORFs) to display in the translations. | Integer 1 or more | 1 | ||||||||||||||||||||||||||||||||||||
| -uppercase | range | Regions to put in uppercase. If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 | Sequence range | If this is left blank, then the sequence case is left alone. | ||||||||||||||||||||||||||||||||||||
| -highlight | range | Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specified as '@filename'. | Sequence range | full sequence | ||||||||||||||||||||||||||||||||||||
| -[no]number | boolean | Number the sequence at the beginning and the end of each line. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -width | integer | Number of nucleotides displayed on each line | Integer 1 or more | 60 | ||||||||||||||||||||||||||||||||||||
| -length | integer | Line length of page (0 for indefinite) | Integer 0 or more | 0 | ||||||||||||||||||||||||||||||||||||
| -margin | integer | Margin around sequence for numbering. | Integer 0 or more | 10 | ||||||||||||||||||||||||||||||||||||
| -[no]name | boolean | Set this to be false if you do not wish to display the ID name of the sequence. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]description | boolean | Set this to be false if you do not wish to display the description of the sequence. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -offset | integer | Number from which you want the DNA sequence to be numbered. | Any integer value | 1 | ||||||||||||||||||||||||||||||||||||
| -html | boolean | Use HTML formatting | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| Associated qualifiers | ||||||||||||||||||||||||||||||||||||||||
| "-sequence" associated sequence qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
| -send1 -send_sequence |
integer | End of the sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||||||||||||||||||||||||||
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||||||||||||||||||||||||||||||||
| -sid1 -sid_sequence |
string | Entryname | Any string | |||||||||||||||||||||||||||||||||||||
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||||||||||||||||||||||||||||||||
| -fformat1 -fformat_sequence |
string | Features format | Any string | |||||||||||||||||||||||||||||||||||||
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||||||||||||||||||||||||||||||||
| "-outfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
| "-outseq" associated seqoutall qualifiers | ||||||||||||||||||||||||||||||||||||||||
| -osformat | string | Output seq format | Any string | |||||||||||||||||||||||||||||||||||||
| -osextension | string | File name extension | Any string | |||||||||||||||||||||||||||||||||||||
| -osname | string | Base file name | Any string | |||||||||||||||||||||||||||||||||||||
| -osdirectory | string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
| -osdbname | string | Database name to add | Any string | |||||||||||||||||||||||||||||||||||||
| -ossingle | boolean | Separate file for each entry | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
| -oufo | string | UFO features | Any string | |||||||||||||||||||||||||||||||||||||
| -offormat | string | Features format | Any string | |||||||||||||||||||||||||||||||||||||
| -ofname | string | Features file name | Any string | |||||||||||||||||||||||||||||||||||||
| -ofdirectory | 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 | ||||||||||||||||||||||||||||||||||||
Input file format
sixpack reads a single nucleotide sequence.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Input files for usage example
'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:x13776
ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC X13776; M43175;
XX
DT 19-APR-1989 (Rel. 19, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS Pseudomonas aeruginosa
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
XX
RN [1]
RP 1167-2167
RA Rice P.M.;
RT ;
RL Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN [2]
RP 1167-2167
RX DOI; 10.1016/0014-5793(89)80249-2.
RX PUBMED; 2495988.
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT Pseudomonas aeruginosa";
RL FEBS Lett. 246(1-2):39-43(1989).
XX
RN [3]
RP 1-1292
RX PUBMED; 1907262.
RA Wilson S., Drew R.;
RT "Cloning and DNA sequence of amiC, a new gene regulating expression of the
RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT product";
RL J. Bacteriol. 173(16):4914-4921(1991).
XX
RN [4]
RP 1-2167
RA Rice P.M.;
RT ;
RL Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR GOA; Q51417.
DR InterPro; IPR003211; AmiSUreI_transpt.
DR UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
[Part of this file has been deleted for brevity]
FT /replace=""
FT /note="ClaI fragment deleted in pSW36, constitutive
FT phenotype"
FT misc_feature 1
FT /note="last base of an XhoI site"
FT misc_feature 648..653
FT /note="end of 658bp XhoI fragment, deletion in pSW3 causes
FT constitutive expression of amiE"
FT conflict 1281
FT /replace="g"
FT /citation=[3]
XX
SQ Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60
ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120
aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180
aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240
agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300
ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360
tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420
agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480
acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540
ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600
gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660
acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720
cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780
ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840
aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900
acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960
tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020
tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080
acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140
gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200
agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260
ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320
cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380
gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440
gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500
gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560
cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620
tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680
gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740
ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800
gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860
aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920
catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980
gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040
gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100
ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160
cctcgag 2167
//
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Output file format
sixpack writes a text report and an ORF sequence file.The output is a standard EMBOSS sequence file.
The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
Output files for usage example
File: x13776.sixpack
X13776
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
G T A G R A S A R S P P A G R R E L H D F1
V P L A E H L L D H H Q P G D G N C T I F2
Y R W P S I C S I T T S R A T G T A R S F3
1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60
----:----|----:----|----:----|----:----|----:----|----:----|
1 ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta 60
P V A P R A D A R D G G A P R R S S C S F6
X Y R Q G L M Q E I V V L R A V P V A R F5
T G S A S C R S S * W W G P S P F Q V I F4
L P G E P G A R A G S L R T A L S D S H F1
Y L A S L E H E R V R F V R R * A T V T F2
T W R A W S T S G F A S Y G A E R Q S Q F3
61 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 120
----:----|----:----|----:----|----:----|----:----|----:----|
61 gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg 120
R G P S G P A R A P E S R V A S L S L * F6
D V Q R A Q L V L P N A E Y P A S R C D F5
* R A L R S C S R T R K T R R Q A V T V F4
R R G N G W D R T R S G R * S A C C S P F1
G E E T D G I A P G A A A D R P A V L R F2
E R K R M G S H Q E R P L I G L L F S E F3
121 aggagaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180
----:----|----:----|----:----|----:----|----:----|----:----|
121 tcctctcctttgcctaccctagcgtggtcctcgccggcgactagccggacgacaagaggc 180
L L P F P H S R V L L P R Q D A Q Q E G F6
C S L F R I P D C W S R G S I P R S N E F5
P S S V S P I A G P A A A S R G A T R R F4
K P A S P P I S S A R T R M A H C S R S F1
N R R H R R Y R A L A R V W R I A R G R F2
T G V T A D I E R S H A Y G A L L A V E F3
181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240
----:----|----:----|----:----|----:----|----:----|----:----|
181 tttggccgcagtggcggctatagctcgcgagcgtgcgcataccgcgtaacgagcgccagc 240
F G A D G G I D L A R V R I A C Q E R D F6
S V P T V A S I S R E C A Y P A N S A T F5
F R R * R R Y R A S A R T H R M A R P R F4
S N * T A R A A S A V A R S K R C P R T F1
[Part of this file has been deleted for brevity]
1981 caacgacccgttctagtcgccagccctccaccgccactagttgaaggaccagccgcacga 2040
T A P C S * R D P P P P S * S G P R R A F6
P Q Q A L D A T P L H R H D V E Q D A H F5
N S P L I L P R S T A T I L K R T P T S F4
E R L R R V L P D L F R S S R A G L A E F1
S A C V A F Y L I F S A A A G Q G S L K F2
A P A S R S T * S F P Q Q P G R A R * R F3
2041 gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100
----:----|----:----|----:----|----:----|----:----|----:----|
2041 ctcgcggacgcagcgcaagatggactagaaaaggcgtcgtcggcccgtcccgagcgactt 2100
S R R R R T R G S R K R L L R A P S A S F6
Q A G A D R E V Q D K G C C G P L A R Q F5
L A Q T A N * R I K E A A A P C P E S F F4
G R S A D P A I R F Y L S V G G R Q P V F1
A G A L T L L F A F T Y L W V A A N Q F F2
P E R * P C Y S L L P I C G W P P T S S F3
2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt 2160
----:----|----:----|----:----|----:----|----:----|----:----|
2101 ccggcctcgcgactgggacgataagcgaaaatggatagacacccaccggcggttggtcaa 2160
P R L A S G A I R K * R D T P P R W G T F6
L G S R Q G Q * E S K G I Q P H G G V L F5
A P A S V R S N A K V * R H T A A L W N F4
P R X F1
L E F2
S X F3
2161 cctcgag 2167
----:--
2161 ggagctc 2220
G R F6
E E L F5
R S F4
##############################
Minimum size of ORFs : 1
Total ORFs in frame 1 : 8
Total ORFs in frame 2 : 5
Total ORFs in frame 3 : 13
Total ORFs in frame 4 : 10
Total ORFs in frame 5 : 16
Total ORFs in frame 6 : 15
Total ORFs : 67
##############################
|
File: x13776.fasta
>X13776_1_ORF1 Translation of X13776 in frame 1, ORF 1, threshold 1, 53aa GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR >X13776_1_ORF2 Translation of X13776 in frame 1, ORF 2, threshold 1, 28aa SACCSPKPASPPISSARTRMAHCSRSSN >X13776_1_ORF3 Translation of X13776 in frame 1, ORF 3, threshold 1, 52aa TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR >X13776_1_ORF4 Translation of X13776 in frame 1, ORF 4, threshold 1, 43aa CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT >X13776_1_ORF5 Translation of X13776 in frame 1, ORF 5, threshold 1, 23aa FATTASGWCSSARTTSIRGKATM >X13776_1_ORF6 Translation of X13776 in frame 1, ORF 6, threshold 1, 72aa CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV ATATAGGRRSPA >X13776_1_ORF7 Translation of X13776 in frame 1, ORF 7, threshold 1, 357aa PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ >X13776_1_ORF8 Translation of X13776 in frame 1, ORF 8, threshold 1, 88aa QEGYRHHAGTGSAVRWRGAVSQCRLVAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSR AGLAEGRSADPAIRFYLSVGGRQPVPRX >X13776_2_ORF1 Translation of X13776 in frame 2, ORF 1, threshold 1, 35aa VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR >X13776_2_ORF2 Translation of X13776 in frame 2, ORF 2, threshold 1, 252aa ATVTGEETDGIAPGAAADRPAVLRNRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNA VPGPRRRPGPLSAVRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLR VFAEHRLRRSGAEPEQCAAGGVPDSPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGA RGNLHSAVSLRRRLAARRRAHLPGARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQP DHQRGGGGEDGE >X13776_2_ORF3 Translation of X13776 in frame 2, ORF 3, threshold 1, 125aa RGRGAGGGRALLLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQ LAGGRRAAAPVRHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRP LCRRA >X13776_2_ORF4 Translation of X13776 in frame 2, ORF 4, threshold 1, 210aa PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP EAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVI TQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDERE AHQHLSREAMKRREPILKIAQELLGNEPSA >X13776_2_ORF5 Translation of X13776 in frame 2, ORF 5, threshold 1, 96aa AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVWLLGKISGREVAVINFLVGVLSACVAF YLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQFLE >X13776_3_ORF1 Translation of X13776 in frame 3, ORF 1, threshold 1, 429aa YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY [Part of this file has been deleted for brevity] SEPMNTTRSP >X13776_5_ORF11 Translation of X13776 in frame 5, ORF 11, threshold 1, 19aa WRIRYAASGALFWFGAGPP >X13776_5_ORF12 Translation of X13776 in frame 5, ORF 12, threshold 1, 10aa TMFGEYSKPS >X13776_5_ORF13 Translation of X13776 in frame 5, ORF 13, threshold 1, 3aa GVG >X13776_5_ORF14 Translation of X13776 in frame 5, ORF 14, threshold 1, 20aa QSSASARSTTGITALRVCDM >X13776_5_ORF15 Translation of X13776 in frame 5, ORF 15, threshold 1, 19aa QPTRNRTPRLRMKSSAHSR >X13776_5_ORF16 Translation of X13776 in frame 5, ORF 16, threshold 1, 107aa RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVTPVSENSRPISGRSWCD PIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQRYX >X13776_6_ORF1 Translation of X13776 in frame 6, ORF 1, threshold 1, 11aa RGTGWRPPTDR >X13776_6_ORF2 Translation of X13776 in frame 6, ORF 2, threshold 1, 36aa KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS >X13776_6_ORF3 Translation of X13776 in frame 6, ORF 3, threshold 1, 7aa SPPPPDR >X13776_6_ORF4 Translation of X13776 in frame 6, ORF 4, threshold 1, 8aa SCPATRRH >X13776_6_ORF5 Translation of X13776 in frame 6, ORF 5, threshold 1, 14aa ETAPRQRTAEPVPA >X13776_6_ORF6 Translation of X13776 in frame 6, ORF 6, threshold 1, 61aa RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLPATGAGAPRARPSHGAASATPWP G >X13776_6_ORF7 Translation of X13776 in frame 6, ORF 7, threshold 1, 23aa SGPGRRCGPGAARSSASASPFPR >X13776_6_ORF8 Translation of X13776 in frame 6, ORF 8, threshold 1, 18aa CAAPIPAQAAPGGHRAAG >X13776_6_ORF9 Translation of X13776 in frame 6, ORF 9, threshold 1, 8aa SRRGTPAR >X13776_6_ORF10 Translation of X13776 in frame 6, ORF 10, threshold 1, 16aa SARAPRGFRTPPAPPG >X13776_6_ORF11 Translation of X13776 in frame 6, ORF 11, threshold 1, 22aa CAESRRRAAQRSRRGGHSGKCW >X13776_6_ORF12 Translation of X13776 in frame 6, ORF 12, threshold 1, 32aa RPRPPARRRLPAAASTGAPNNRCGSAARPGRR >X13776_6_ORF13 Translation of X13776 in frame 6, ORF 13, threshold 1, 5aa PPPAG >X13776_6_ORF14 Translation of X13776 in frame 6, ORF 14, threshold 1, 407aa GPAPATRAGCRAASWRSWERSPAHAGGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFR DARRQAAVVVLALHPDRPLWRVDVDVVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGG DGRVLREETMAGLDEGPAGGRIDAGEVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAV AVATGDGAIQLGGAGAHHGGEDHVGARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQ VAHHMVAFPRIDVVRADEHHPLAVVANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVA EQRVGALDHRHHRLARVRHVAAHEEPYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADA ALAVQLLDREQCAIRVRALDIGGDAGFGEQQADQRPLLVRSHPFPLL >X13776_6_ORF15 Translation of X13776 in frame 6, ORF 15, threshold 1, 39aa LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPAVP |
Data files
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata
The Genetic Code data files are based on the NCBI genetic code tables. Their names and descriptions are:
- EGC.0
- Standard (Differs from GC.1 in that it only has initiation site 'AUG')
- EGC.1
- Standard
- EGC.2
- Vertebrate Mitochodrial
- EGC.3
- Yeast Mitochondrial
- EGC.4
- Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
- EGC.5
- Invertebrate Mitochondrial
- EGC.6
- Ciliate Macronuclear and Dasycladacean
- EGC.9
- Echinoderm Mitochondrial
- EGC.10
- Euplotid Nuclear
- EGC.11
- Bacterial
- EGC.12
- Alternative Yeast Nuclear
- EGC.13
- Ascidian Mitochondrial
- EGC.14
- Flatworm Mitochondrial
- EGC.15
- Blepharisma Macronuclear
- EGC.16
- Chlorophycean Mitochondrial
- EGC.21
- Trematode Mitochondrial
- EGC.22
- Scenedesmus obliquus
- EGC.23
- Thraustochytrium Mitochondrial
The format of these files is very simple.
It consists of several lines of optional comments, each starting with a '#' character.
These are followed the line: 'Genetic Code [n]', where 'n' is the number of the genetic code file.
This is followed by the description of the code and then by four lines giving the IUPAC one-letter code of the translated amino acid, the start codons (indicdated by an 'M') and the three bases of the codon, lined up one on top of the other.
For example:
------------------------------------------------------------------------------ # Genetic Code Table # # Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html # and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c # # Differs from Genetic Code [1] only in that the initiation sites have been # changed to only 'AUG' Genetic Code [0] Standard AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts = -----------------------------------M---------------------------- Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG ------------------------------------------------------------------------------
Notes
An open reading frame is defined in this program as any possible translation between two STOP codons. Optionally, the beginning or end of a sequence may be counted as an ORF even if it's less than the minimal ORF size or (end only) lacking a STOP codon. See the -firstorf and -lastorf options.
References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| abiview | Display the trace in an ABI sequencer file |
| backtranambig | Back-translate a protein sequence to ambiguous nucleotide sequence |
| backtranseq | Back-translate a protein sequence to a nucleotide sequence |
| checktrans | Reports STOP codons and ORF statistics of a protein |
| cirdna | Draws circular maps of DNA constructs |
| coderet | Extract CDS, mRNA and translations from feature tables |
| getorf | Finds and extracts open reading frames (ORFs) |
| iep | Calculate the isoelectric point of proteins |
| lindna | Draws linear maps of DNA constructs |
| marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
| pepinfo | Plot amino acid properties of a protein sequence in parallel |
| pepnet | Draw a helical net for a protein sequence |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| plotorf | Plot potential open reading frames in a nucleotide sequence |
| prettyplot | Draw a sequence alignment with pretty formatting |
| 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 |
| showpep | Displays protein sequences with features in pretty format |
| showseq | Displays sequences with features in pretty format |
| syco | Draw synonymous codon usage statistic plot for a nucleotide sequence |
| tcode | Identify protein-coding regions using Fickett TESTCODE statistic |
| transeq | Translate nucleic acid sequences |
| wobble | Plot third base position variability in a nucleotide sequence |
Author(s)
Thomas Laurent formerly at:Lion Bioscience Ltd, Compass House, 80-82 Newmarket Road, Cambridge, CB5 8DZ, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.