|
|
sixpack |
It also writes a file containing the open reading frames that are larger than the specified minimum size (default 1 base, showing all possible open reading frames). These open reading frames are written as protein sequences in the default output sequence format.
An open reading frame is defined in this program as any possible translation between two STOP codons.
% sixpack Display a DNA sequence with 6-frame translation and ORFs Input sequence: tembl:paamir Output file [paamir.sixpack]: Output sequence [paamir.fasta]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers:
[-sequence] sequence Sequence USA
[-outfile] outfile If you enter the name of a file here then
this program will write the sequence details
into that file.
-outseq seqoutall If you enter the name of a file here then
this program will write the ORFs into that
file.
Optional qualifiers:
-table menu Genetics code used for the translation
-[no]firstorf boolean Count the beginning of a sequence as a
possible ORF, even if it's inferior to the
minimal ORF size.
-[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.
-mstart boolean Displays only ORFs starting with an M.
Advanced qualifiers:
-[no]reverse boolean Display also the translation of the DNA
sequence in the 3 reverse frames
-orfminsize integer Minimum size of Open Reading Frames (ORFs)
to display in the translations.
-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
-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 specifed as '@filename'.
-[no]number boolean Number the sequence at the beginning and the
end of each line.
-width integer Number of nucleotides displayed on each line
-length integer Line length of page (0 for indefinite)
-margin integer Margin around sequence for numbering.
-[no]name boolean Set this to be false if you do not wish to
display the ID name of the sequence.
-[no]description boolean Set this to be false if you do not wish to
display the description of the sequence.
-offset integer Number from which you want the DNA sequence
to be numbered.
-html boolean Use HTML formatting
Associated qualifiers:
"-sequence" related qualifiers
-sbegin1 integer First base used
-send1 integer Last base used, def=seq length
-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
-sopenfile1 string Input filename
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" related qualifiers
-odirectory2 string Output directory
"-outseq" related qualifiers
-osformat string Output seq format
-osextension string File name extension
-osname string Base file name
-osdirectory string Output directory
-osdbname string Database name to add
-ossingle boolean Separate file for each entry
-oufo string UFO features
-offormat string Features format
-ofname string Features file name
-ofdirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for required and optional values
-debug boolean Write debug output to program.dbg
-acdlog boolean Write ACD processing log to program.acdlog
-acdpretty boolean Rewrite ACD file as program.acdpretty
-acdtable boolean Write HTML table of options
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Mandatory qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required | ||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) |
If you enter the name of a file here then this program will write the sequence details into that file. | Output file | <sequence>.sixpack | ||||||||||||||||||||||||||||||||||||
| -outseq | If you enter the name of a file here then this program will write the ORFs into that file. | Writeable sequence(s) | <sequence>.format | ||||||||||||||||||||||||||||||||||||
| Optional qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -table | Genetics code used for the translation |
|
0 | ||||||||||||||||||||||||||||||||||||
| -[no]firstorf | 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 | 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 | Displays only ORFs starting with an M. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
| Advanced qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -[no]reverse | Display also the translation of the DNA sequence in the 3 reverse frames | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -orfminsize | Minimum size of Open Reading Frames (ORFs) to display in the translations. | Integer 1 or more | 1 | ||||||||||||||||||||||||||||||||||||
| -uppercase | 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 | 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 specifed as '@filename'. | Sequence range | full sequence | ||||||||||||||||||||||||||||||||||||
| -[no]number | Number the sequence at the beginning and the end of each line. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -width | Number of nucleotides displayed on each line | Integer 1 or more | 60 | ||||||||||||||||||||||||||||||||||||
| -length | Line length of page (0 for indefinite) | Integer 0 or more | 0 | ||||||||||||||||||||||||||||||||||||
| -margin | Margin around sequence for numbering. | Integer 0 or more | 10 | ||||||||||||||||||||||||||||||||||||
| -[no]name | 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 | Set this to be false if you do not wish to display the description of the sequence. | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -offset | Number from which you want the DNA sequence to be numbered. | Any integer value | 1 | ||||||||||||||||||||||||||||||||||||
| -html | Use HTML formatting | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
ID PAAMIR standard; DNA; PRO; 2167 BP.
XX
AC X13776; M43175;
XX
SV X13776.1
XX
DT 19-APR-1989 (Rel. 19, Created)
DT 17-FEB-1997 (Rel. 50, Last updated, Version 22)
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; gamma subdivision; 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 MEDLINE; 89211409.
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
RT aeruginosa";
RL FEBS Lett. 246:39-43(1989).
XX
RN [3]
RP 1-1292
RX MEDLINE; 91317707.
RA Wilson S., Drew R.;
RT "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT product.";
RL J. Bacteriol. 173:4914-4921(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 SWISS-PROT; P10932; AMIR_PSEAE.
DR SWISS-PROT; P27017; AMIC_PSEAE.
DR SWISS-PROT; Q51417; AMIS_PSEAE.
[Part of this file has been deleted for brevity]
FT phenotype"
FT /replace=""
FT /gene="amiC"
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
//
|
>PAAMIR_1_ORF1 Translation of PAAMIR in frame 1, ORF 1, threshold 1, 53aa GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR >PAAMIR_1_ORF2 Translation of PAAMIR in frame 1, ORF 2, threshold 1, 28aa SACCSPKPASPPISSARTRMAHCSRSSN >PAAMIR_1_ORF3 Translation of PAAMIR in frame 1, ORF 3, threshold 1, 52aa TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR >PAAMIR_1_ORF4 Translation of PAAMIR in frame 1, ORF 4, threshold 1, 43aa CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT >PAAMIR_1_ORF5 Translation of PAAMIR in frame 1, ORF 5, threshold 1, 23aa FATTASGWCSSARTTSIRGKATM >PAAMIR_1_ORF6 Translation of PAAMIR in frame 1, ORF 6, threshold 1, 72aa CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV ATATAGGRRSPA >PAAMIR_1_ORF7 Translation of PAAMIR in frame 1, ORF 7, threshold 1, 357aa PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ >PAAMIR_1_ORF8 Translation of PAAMIR in frame 1, ORF 8, threshold 1, 88aa QEGYRHHAGTGSAVRWRGAVSQCRLVAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSR AGLAEGRSADPAIRFYLSVGGRQPVPRX >PAAMIR_2_ORF1 Translation of PAAMIR in frame 2, ORF 1, threshold 1, 35aa VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR >PAAMIR_2_ORF2 Translation of PAAMIR in frame 2, ORF 2, threshold 1, 252aa ATVTGEETDGIAPGAAADRPAVLRNRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNA VPGPRRRPGPLSAVRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLR VFAEHRLRRSGAEPEQCAAGGVPDSPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGA RGNLHSAVSLRRRLAARRRAHLPGARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQP DHQRGGGGEDGE >PAAMIR_2_ORF3 Translation of PAAMIR in frame 2, ORF 3, threshold 1, 125aa RGRGAGGGRALLLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQ LAGGRRAAAPVRHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRP LCRRA >PAAMIR_2_ORF4 Translation of PAAMIR in frame 2, ORF 4, threshold 1, 210aa PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP EAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVI TQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDERE AHQHLSREAMKRREPILKIAQELLGNEPSA >PAAMIR_2_ORF5 Translation of PAAMIR in frame 2, ORF 5, threshold 1, 96aa AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVWLLGKISGREVAVINFLVGVLSACVAF YLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQFLE >PAAMIR_3_ORF1 Translation of PAAMIR in frame 3, ORF 1, threshold 1, 429aa YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY [Part of this file has been deleted for brevity] SEPMNTTRSP >PAAMIR_5_ORF11 Translation of PAAMIR in frame 5, ORF 11, threshold 1, 19aa WRIRYAASGALFWFGAGPP >PAAMIR_5_ORF12 Translation of PAAMIR in frame 5, ORF 12, threshold 1, 10aa TMFGEYSKPS >PAAMIR_5_ORF13 Translation of PAAMIR in frame 5, ORF 13, threshold 1, 3aa GVG >PAAMIR_5_ORF14 Translation of PAAMIR in frame 5, ORF 14, threshold 1, 20aa QSSASARSTTGITALRVCDM >PAAMIR_5_ORF15 Translation of PAAMIR in frame 5, ORF 15, threshold 1, 19aa QPTRNRTPRLRMKSSAHSR >PAAMIR_5_ORF16 Translation of PAAMIR in frame 5, ORF 16, threshold 1, 107aa RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVTPVSENSRPISGRSWCD PIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQRYX >PAAMIR_6_ORF1 Translation of PAAMIR in frame 6, ORF 1, threshold 1, 11aa RGTGWRPPTDR >PAAMIR_6_ORF2 Translation of PAAMIR in frame 6, ORF 2, threshold 1, 36aa KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS >PAAMIR_6_ORF3 Translation of PAAMIR in frame 6, ORF 3, threshold 1, 7aa SPPPPDR >PAAMIR_6_ORF4 Translation of PAAMIR in frame 6, ORF 4, threshold 1, 8aa SCPATRRH >PAAMIR_6_ORF5 Translation of PAAMIR in frame 6, ORF 5, threshold 1, 14aa ETAPRQRTAEPVPA >PAAMIR_6_ORF6 Translation of PAAMIR in frame 6, ORF 6, threshold 1, 61aa RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLPATGAGAPRARPSHGAASATPWP G >PAAMIR_6_ORF7 Translation of PAAMIR in frame 6, ORF 7, threshold 1, 23aa SGPGRRCGPGAARSSASASPFPR >PAAMIR_6_ORF8 Translation of PAAMIR in frame 6, ORF 8, threshold 1, 18aa CAAPIPAQAAPGGHRAAG >PAAMIR_6_ORF9 Translation of PAAMIR in frame 6, ORF 9, threshold 1, 8aa SRRGTPAR >PAAMIR_6_ORF10 Translation of PAAMIR in frame 6, ORF 10, threshold 1, 16aa SARAPRGFRTPPAPPG >PAAMIR_6_ORF11 Translation of PAAMIR in frame 6, ORF 11, threshold 1, 22aa CAESRRRAAQRSRRGGHSGKCW >PAAMIR_6_ORF12 Translation of PAAMIR in frame 6, ORF 12, threshold 1, 32aa RPRPPARRRLPAAASTGAPNNRCGSAARPGRR >PAAMIR_6_ORF13 Translation of PAAMIR in frame 6, ORF 13, threshold 1, 5aa PPPAG >PAAMIR_6_ORF14 Translation of PAAMIR in frame 6, ORF 14, threshold 1, 407aa GPAPATRAGCRAASWRSWERSPAHAGGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFR DARRQAAVVVLALHPDRPLWRVDVDVVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGG DGRVLREETMAGLDEGPAGGRIDAGEVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAV AVATGDGAIQLGGAGAHHGGEDHVGARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQ VAHHMVAFPRIDVVRADEHHPLAVVANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVA EQRVGALDHRHHRLARVRHVAAHEEPYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADA ALAVQLLDREQCAIRVRALDIGGDAGFGEQQADQRPLLVRSHPFPLL >PAAMIR_6_ORF15 Translation of PAAMIR in frame 6, ORF 15, threshold 1, 39aa LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPAVP |
PAAMIR
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 F3
2161 cctcgag 2167
----:----|----:----|----:----|----:----|----:----|----:----|
2161 ggagctc 2167
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
##############################
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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:
The Genetic Code data files are based on the NCBI genetic code tables. Their names and descriptions are:
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 ------------------------------------------------------------------------------
| Program name | Description |
|---|---|
| abiview | Reads ABI file and display the trace |
| backtranseq | Back translate a protein sequence |
| cirdna | Draws circular maps of DNA constructs |
| coderet | Extract CDS, mRNA and translations from feature tables |
| getorf | Finds and extracts open reading frames (ORFs) |
| lindna | Draws linear maps of DNA constructs |
| marscan | Finds MAR/SAR sites in nucleic sequences |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| plotorf | Plot potential open reading frames |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| prettyseq | Output sequence with translated ranges |
| remap | Display a sequence with restriction cut sites, translation etc |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| showfeat | Show features of a sequence |
| showorf | Pretty output of DNA translations |
| showseq | Display a sequence with features, translation etc |
| syco | Synonymous codon usage Gribskov statistic plot |
| tcode | Fickett TESTCODE statistic to identify protein-coding DNA |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |
| transeq | Translate nucleic acid sequences |
| wobble | Wobble base plot |