transeq |
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transeq reads one or more nucleotide sequences and writes the corresponding protein sequence translations to file. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames. The translation may be restricted to specified regions, for example, corresponding to the coding regions of your sequences. It can translate using the standard ('Universal') genetic code and also with a selection of non-standard codes.
To translate a sequence in the first frame (starting at the first base and proceeding to the end):
% transeq tembl:x13776 amir.pep Translate nucleic acid sequences |
Go to the input files for this example
Go to the output files for this example
Example 2
To translate a sequence in the second frame:
% transeq tembl:x13776 amir.pep -frame=2 Translate nucleic acid sequences |
Go to the output files for this example
Example 3
To translate a sequence in the first frame in the reverse sense (starting at the last frame 1 codon and proceeding to the start):
% transeq tembl:x13776 amir.pep -frame=-1 Translate nucleic acid sequences |
Go to the output files for this example
Example 4
To translate a sequence in all three forward frames:
% transeq tembl:x13776 amir.pep -frame=F Translate nucleic acid sequences |
Go to the output files for this example
Example 5
To translate a sequence in all three reverse frames:
% transeq tembl:x13776 amir.pep -frame=R Translate nucleic acid sequences |
Go to the output files for this example
Example 6
To translate a sequence in all six forward and reverse frames:
% transeq tembl:x13776 amir.pep -frame=6 Translate nucleic acid sequences |
Go to the output files for this example
Example 7
To translate a specific set of regions corresponding to a known set of coding sequences:
% transeq tembl:x13776 amir.pep -reg=2-45,67-201,328-509 Translate nucleic acid sequences |
Go to the output files for this example
Example 8
To translate a mitochondrial sequence using the mammalian mitochondrion genetic code table:
% transeq mito.seq mito.pep -table 2 Translate nucleic acid sequences |
Go to the input files for this example
Go to the output files for this example
Translate nucleic acid sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outseq] seqoutall [ |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||||||
[-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | ||||||||||||||||||||||||||||||||||||
[-outseq] (Parameter 2) |
seqoutall | Protein sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format | ||||||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||||||
-frame | list | Frame(s) to translate |
|
1 | ||||||||||||||||||||||||||||||||||||
-table | list | Code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
-regions | range | Regions to translate. If this is left blank, then the complete sequence is translated. 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 Note: you should not try to use this option with any other frame than the default, -frame=1 | Sequence range | Whole sequence | ||||||||||||||||||||||||||||||||||||
-trim | boolean | This removes all 'X' and '*' characters from the right end of the translation. The trimming process starts at the end and continues until the next character is not a 'X' or a '*' | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
-clean | boolean | This changes all STOP codon positions from the '*' character to 'X' (an unknown residue). This is useful because some programs will not accept protein sequences with '*' characters in them. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||||||
-alternative | boolean | The default definition of frame '-1' is the reverse-complement of the set of codons used in frame 1. (Frame -2 is the set of codons used by frame 2, similarly frames -3 and 3). This is a common standard, used by the Staden package and other programs. If you prefer to define frame '-1' as using the set of codons starting with the last codon of the sequence, then set this to be true. | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||
Associated qualifiers | ||||||||||||||||||||||||||||||||||||||||
"-sequence" associated seqall qualifiers | ||||||||||||||||||||||||||||||||||||||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||||||||||||||||||||||||||
-send1 -send_sequence |
integer | End of each 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 | |||||||||||||||||||||||||||||||||||||
"-outseq" associated seqoutall qualifiers | ||||||||||||||||||||||||||||||||||||||||
-osformat2 -osformat_outseq |
string | Output seq format | Any string | |||||||||||||||||||||||||||||||||||||
-osextension2 -osextension_outseq |
string | File name extension | Any string | |||||||||||||||||||||||||||||||||||||
-osname2 -osname_outseq |
string | Base file name | Any string | |||||||||||||||||||||||||||||||||||||
-osdirectory2 -osdirectory_outseq |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||||||
-osdbname2 -osdbname_outseq |
string | Database name to add | Any string | |||||||||||||||||||||||||||||||||||||
-ossingle2 -ossingle_outseq |
boolean | Separate file for each entry | Boolean value Yes/No | N | ||||||||||||||||||||||||||||||||||||
-oufo2 -oufo_outseq |
string | UFO features | Any string | |||||||||||||||||||||||||||||||||||||
-offormat2 -offormat_outseq |
string | Features format | Any string | |||||||||||||||||||||||||||||||||||||
-ofname2 -ofname_outseq |
string | Features file name | Any string | |||||||||||||||||||||||||||||||||||||
-ofdirectory2 -ofdirectory_outseq |
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 |
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.
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 // |
>gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete genome GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGCT TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATTT GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAAC TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGACA GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACATG AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAGC CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATCC CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCTC GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTTA AGGGTTGGTAAACTTCGTGCCAGCCACCGCGGTCATACGATCGACCCAAATTAATAGAAGCACGGCGTAAAGAGTGTTAA GGAGCCACATGAAATAAAGTCAAACCTTAATTAAGCTGTAAAAAGCCCTAATTAAAATTAAGCCAAACTACGAAAGTGAC TTTAATATAATCTGATCACACGACAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGTCGTAAACCCCAAT AGTCACAAAACAAGACTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTTGGCGGTGCCTCATACCCA TCTAGAGGAGCCTGTTCTGTAACCGATAAACCCCGATCAACCTCACCAACCCTTGCTACTTCAGTCTATATACCGCCATC TTCAGCAAACCCTAAAGGGAGAAAAGTAAGCATAACCATCCTACATAAAAACGTTAGGTCAAGGTGTAACCCATGGGTTG GGAAGTAATGGGCTACATTTTCTAAGCTAAGAACATCCCCTATACTCACACGAAAGTTTTTATGAAACTTAAAAACTAAA GGAGGATTTAGTAGTAAATCAAGAGCAGAGTGCTTGATTGAATAAGGCCATGAGGGCACGCACACACCGCCCGTCACCCT CCTCAAGTACCCCAGCTATAAACCCCAGTTCGTTAACTCAGGCCAAGCAATTATACGAGAGGAGACAAGTCGTAACAAGG TAAGCATACCGGAAGGTGTGCTTGGACAAAACAAGATATAGCTTAAACAAAGCATGTAGTTTACACCTAGAAGATTCCAC AGCCCGTGTATATCTTGAACTAGCCCTAGCCCACACCCTCCCCACCTCTACTACCACAAATCAATCAAATAAAACATTTA CCATCCCTTCAAAGTATAGGAGATAGAAATTTAAATATCAGTGGCGCTATAGAGATAGTACCGTAAGGAAAGATGAAAGA AAAACCTAAAAGTAATAAAAAGCAAAGCTTACCACTTGTACCTTTTGCATAATGACTTAACTAGTAATAAATTAGCAAAG AGACCTTAAGTTAAATTACCCGAAACCAGACGAGCTACTTATGAGCAGCACCTAGAACGAACTCATCTATGTGGCAAAAT AGTGAGAAGACTTATAAGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTGTCCCTGAAAAGAATCTCAGTTC AACATTAAATAATACTAAAAGCCCATGCCAAGCCTTAACGTATATTTAACTGTTAATCTAAAAAGGTACAGCTTTTTAGA AATGGGTACAACCTTGACTAGAGAGTAAAATCAAACATAAACATAGTTGGCCTAAAAGCAGCCATCAATTAAGAAAGCGT TCAAGCTCGACAACAAAATAATGTTTTAATTCCAACATTAAGTAAATCAACTCCTAGCCTGACTATTGGACTAATCTATA CAAATATAGAAGCAATACTGTTAATATGAGTAACAAGAAATTTTTCTCCTAGCACAAGCTTACACCAGTAACTGATAATA TACTGATAATTAACAGCAAATAAATAAAACCCAACACTAAATTATTTATTAAAATACTGTTAACCCAACACAGGCGTGCA TTAAGGAAAGATTAAAAAAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCAT AACCAGTATTAGAGCACTGCCTGCCCGGTGACTAATCGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAAT CACTTGTTCTCTAATTAGGGACTTGTATGAATGGCCACACGAGGGTTTTACTGTCTCTTACTTTTAATCAGTGAAATTGA CCTCTCCGTGAAGAGGCGGAGATAACAAAATAAGACGAGAAGACCCTATGGAGCTTCAATTAATCAACCCAAAAACCATA ACCTTAAACCACCAAGGGATAACAAAACCTTATATGGGCTGACAATTTCGGTTGGGGTGACCTCGGAGTACAAAAAACCC TCCGAGTGATTAAAACTTAGGCCCACTAGCCAAAGTACAATATCACTTATTGATCCAATCCTTTGATCAACGGAACAAGT TACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGATCAGGAC ATCCTAATGGTGCAGCTGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTA ATCCAGGTCGGTTTCTATCTATTACGCATTTCTCCCAGTACGAAAGGACAAGAGAAATAAGGCCAACTTCAAACAAGCGC CTTCAAACAATTAATGACCTAGTCTCAACTTAATAATTAAGCGCAAACAAACCTGCCCAAGACCAGGGCCTTGTTGAGGT GGCAGAGTTCGGTAATTGCATAAAACTTAAACTTTTACACCCAGAGGTTCAAATCCTCTCCCCAACAAAATGTTTATAAT TAACATTCTAACACTCATTCTCCCCATCCTCCTAGCCGTAGCATTCCTAACGCTAGTAGAACGCAAAATTCTAGGCTATA TGCAGTTCCGAAAGGGGCCAAACATCGTAGGCCCACATGGCTTACTCCAACCCTTTGCCGATGCAATTAAATTATTCACT AAAGAACCCCTACGGCCAGCTACATCCTCAACTACTATGTTTATCATTGCACCAGTACTAGCCCTAACCCTGGCCCTCAC TATATGAAGCCCCCTACCCATACCATACCCCCTCATTAACATAAACCTAGGAGTATTATTCATATTAGCAATATCCAGCC TAGCCGTCTACTCCATCCTATGATCAGGCTGAGCCTCCAACTCAAAATACGCACTAATTGGAGCCCTACGAGCAGTAGCA CAAACAATCTCATATGAGGTAACACTAGCCATTATCCTCCTATCAGTACTCCTAATAAACGGCTCCTACACCTTATCAAC ATTAGCCACAACACAAGAACAACTATGATTACTATTCCCATCATGACCCTTAGCCATAATGTGATTCATCTCCACCCTAG CAGAAACTAATCGAGCTCCTTTTGATCTAACAGAGGGAGAATCAGAACTCGTATCAGGCTTCAACGTAGAATATGCAGCA GGCCCTTTCGCCCTATTCTTCCTGGCAGAATACGCCAACATCATTATAATGAATATACTCACAGCCATTTTATTCCTAGG [Part of this file has been deleted for brevity] CATTGTCTTCTGCGCCTTCATCACTAGTCTAGTTCCCGCAATAGTATATCTTCACACAAACCAAGAAACACTCATCTCAA ACTGACACTGAATCACAATCCAAACCCTCAAACTAACACTTAGCTTTAAAATAGATTACTTTTCACTTATATTTATACCA GTAGCACTATTCATTACATGATCCATCATAGAATTCTCAATATGATATATGCACTCCGACCCCTACATCAACCAATTTTT TAAATACTTACTCCTCTTCCTCATCACCATACTAATCCTTGTTACAGCTAACAATCTCTTCCAACTTTTCATCGGATGAG AAGGAGTAGGAATTATATCCTTCTTACTAATTGGCTGATGATTCGGACGAACAGATGCAAATACAGCCGCCCTCCAAGCA ATCCTATACAATCGTATCGGAGACATTGGACTCCTTGCATCAATAGCATGATTTCTCTCTAATATAAACACATGAGACCT AGAACAAATCTTTATACTCAACCAAAACCCCTTAAATTTCCCCCTCATAGGACTCGTACTAGCCGCAGCAGGAAAATCGG CTCAATTCGGACTCCACCCTTGACTCCCATCAGCAATAGAAGGTCCTACCCCAGTCTCAGCCCTACTCCACTCAAGCACA ATAGTTGTAGCAGGAATCTTCTTGCTTGTCCGCTTCTACCCATTAATAGAAAATAACAAGCTAATCCAAACAGTAACCCT CTGCTTAGGCGCTATCACAACTCTATTTACAGCCATCTGTGCCCTCACCCAAAACGACATCAAAAAAATTATTGCTTTCT CCACCTCCAGCCAGCTAGGCCTAATAATAGTAACAATCGGCCTTAACCAACCTTACCTAGCATTCCTACACATTTGCACA CACGCCTTCTTTAAAGCTATACTATTCCTATGTTCTGGCTCCATCATCCATAACCTAAACAACGAACAAGATATCCGAAA AATAGGAGGGCTATTTAAGGCCCTCCCATTCACCACAACCGCCCTTATCATCGGATGTCTTGCACTAACAGGAATGCCAT TCCTGACCGGATTCTACTCCAAAGATCCCATTATTGAAGCCGCCACTTCGTCTTATACCAACGCCTGAGCCCTATTACTG ACCTTAATCGCCACCTCCCTTACGGCCGTCTATAGCACCCGCATCATTTTCTTTGCACTACTAGGACAACCCCGCTTCCC TCCCTCCACAACCATTAACGAAAATAATCCACTGTTAATCAACCCTATCAAACGACTACTCGTCGGAAGTATCTTCGCTG GCTTCATCCTATCCAACAGTATTCCCCCAATAACTACACCTTTAATAACCATACCCCTGCACTTAAAATTAACCGCCCTT GCAATAACAACCCTAGGCTTCATCATCGCATTCGAAATTAACCTTGACACACAAAATCTAAAGCACAAGCACCCATCAAA CTCCTTTAAATTCTCCACCTTACTAGGTTATTTCCCCACAATCATACATCGCCTACCCCCTCACCTTGACCTGTTAATAA GCCAAAAACTAGCAACTTCCCTACTAGATCTAACTTGACTAGAAACTATTTTACCAAAAACCACAGCCCTTATCCAACTA AAAGCCTCTACACTAACCTCTAACCAACAAGGCCTCATCAAACTCTACTTCTTATCTTTCCTCATCACCATCACCCTCAG CATAATCTTATTTAACTACCCCGAGTAATCTCCATAATAATTACAACACTAATAAATAAAGACCAACCCGTAACAATCAC CAACCAAACACCATAACTATATAATGCCGCAATCCCTGTAGCCTCCTCACTAAAAACCCCAGAACCCCCAGTATCATAAA CAACCCAGTCCCCTAGTCCATCAAACTCAAACATAATCTTCACCTCCCCACTCTTCAAAGCATAAATCACAATTAAAAAC TCCACCACCAACCCTAAAACAAATGCTCCTAGTACAACTTTATTAGAAACCCAAACCTCAGGATACTGTTCAGTAGCCAT AGCTGTTGTATAACCAAATACTACCAGCATTCCCCCCAAATAAATCAAAAACACCATTAACCCCAAAAACGAACCACCAA AACTCAAAATAACTCCACATCCAACACCACCACCCACAATCAACCCTAAACCCCCATAAATAGGTGAAGGCTTTGAAGAA ACCCCCACAAAACTAATTACAAAAATAATACTTAAAATGAAAACAATATACATTATCATTATTCTCACATGGACTTCAAC CATGACCAATGACATGAAAAATCATCGTTGTTATTCAACTACAAGAACACCAATGACCAACATCCGAAAAACACACCCAC TAATAAAAATCGTCAACGACGCATTCGTCGATCTCCCCACCCCATCAAATATCTCTTCATGATGGAACTTCGGCTCCCTA CTCGGCCTCTGCTTAATTATACAAATCCTAACAGGCCTATTCCTAGCAATACACTACACACCAGACACAACAACCGCCTT CTCATCAGTCACACACATCTGCCGAGACGTGAATTACGGCTGAATTATCCGATACCTACATGCAAATGGGGCTTCTATAT TCTTCATCTGCCTCTACGCTCACATAGGACGAGGCCTATACTACGGCTCCTACGCCTTCCGAGAAACATGAAATATTGGA GTTATTCTACTATTCACAGTTATAGCCACCGCATTCGTAGGCTACGTCCTGCCCTGAGGACAAATATCATTCTGAGGCGC AACTGTAATCACTAACCTCCTATCAGCAATCCCATACATTGGTACCACCCTAGTCGAATGAATCTGAGGCGGTTTCTCTG TAGATAAAGCAACACTAACACGCTTTTTTGCCTTTCACTTTATCCTCCCCTTCATCATCCTAGCATTAGCAATTGTCCAC CTTATTTTCCTTCACGAAACAGGATCCAACAACCCCACAGGCATCCCATCCGACATAGATAAAATCCCATTCCACCCCTA CCACACAATTAAAGACATTCTAGGTGCCCTATTACTAATCCTAATCCTACTAATACTAACCCTATTCGCACCCGACCTAC TTGGAGACCCAGACAACTATACCCCAGCAAACCCACTCAGTACCCCAGCACACATTAAACCAGAATGGTATTTTCTATTC GCATACGCAATCCTACGATCAATCCCCAACAAACTAGGCGGAGTCTTAGCCCTACTACTCTCAATCCTAATCCTAGCCTT CATCCCAATACTCCACACATCCAATCAACGAAGCATAATATTTCGACCCTTTAGCCAGTTCTTGTTCTGAGTCCTAGTCG CAGATCTACTAACCCTAACATGGATCGGCGGCCAACCAGTAGAACACCCCTACATAATTGTAGGCCAACTCGCATCCATC CTCTATTTCCTCTTAATTCTAGTATTAATACCAGTAACTAGTCTTATCGAGAACAAACTTATAAAATGAAGAGTCTTTGT AGTATAATTAAATACCCCGGTTTTGTAAACCGGAAAAGGAGACAAGACACACCTCCCTAAGACTCAAGGAAGAAGTATTA CACTCCACCATCAGCACCCAAAGCTGAAGTTCTACATAAACTATTCCCTGAAAAAGTATATTGTACAATAACCACAGGAC CACAGTACTATGTCCGTATTGAAAATAACTTGCCTTATTAGATATTATTATGTAACTCGTGCATGCATGTACTTCCACAT AATTAATAGCGTCTTTCCATGGGTATGAACAGATATACATGCTATGTATAATTGTGCATTCAATTATTTTCACCACGAGC AGTTGAAGCTCGTATTAAATTTTATTAATTTTACATATTACATAATATGTATTAATAGTACAATAGCGCATGTTCTTATG CATCCCCAGATCTATTTAAATCAAATGATTCCTATGGCCGCTCCATTAGATCACGAGCTTAGTCAGCATGCCGCGTGAAA CCAGCAACCCGCTTGGCAGGGATCCCTCTTCTCGCACCGGGCCCATCACTCGTGGGGGTAGCTATTTAATGATCTTTATA AGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTCGTTCCCCTTAAATAAGACATCTCGATGG |
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.
>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV PRX |
>X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF LE |
>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS GT |
>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV PRX >X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF LE >X13776_3 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY DIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWS ASMGGGPLP*APTRCSAACASCRCWSSTRRGRSATPWSCS*SASVVRCASAGRRRKPSTC RWTWSSPAFSRMATTTRSLRCSPPGLRALPWWRWWSTKAPRCSRRSSSWSATA*SPSRSM PTGCCLCWYRRGASARKWRS*SRRPSSSRTASPARPGSTRPRCC*CSAMAGTSARRTSTC RGKR*SGASRS*RSLRSCWETSRPPERSGPTRTITRGVSSSCWDWFCCTLARCCFSMPSG CWARSAVGRWR*STSWSAC*APASRST*SFPQQPGRAR*RPER*PCYSLLPICGWPPTSS SX |
>X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS GT >X13776_5 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation LEELVGGHPQIGKSE*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA QQPDGIEKQHRANVQQNQSQHDDDTPLVIVLVGPDRSGGRLVSQQLLSDLQDRLAPLHRF PRQVLVRLALVPAMALHQQHLGLVDPGLAGDAVLELLGLLLQLRHFLADAPRRYQHRQHP VGIERLGDHAVALQLDDLREHRGAFVLHQRHQGSARSPGGEQRSDLVVVAILENAGEDHV HRHVEGFRRRPALAHRTTDADQLQDQGVADLPRRVEDQHLQLAQAAEQRVGAHGSGPPPM LADQSSRLCTTT*GSGRIGSGDCQRTWNTPRASISAMREDRRLWLFWRSTRTGPCGASMS MSYRCRCTSSTRQLPAACAARPSNKVCQ*AASAQAVMVAFSGKKPWQAWTKARLAGVSML EK*GATTTCPSATSLSIFATSASLVVRLAIGGRLPSP*RRAMARYSSAVPVPTTVEKTTS ARAW*MRSTARCKSSSEGYSGM*ISSSTVPPCWRYRWRITWLLSRG*M*SEPMNTTRSP* WRIRYAASGALFWFGAGPP*TMFGEYSKPS*GVG*QSSASARSTTGITALRVCDM*QPTR NRTPRLRMKSSAHSR*RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVT PVSENSRPISGRSWCDPIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQ RYX >X13776_6 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation RGTGWRPPTDR*KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS*SPPPPDR*SCP ATRRH*ETAPRQRTAEPVPA**RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLP ATGAGAPRARPSHGAASATPWPG*SGPGRRCGPGAARSSASASPFPR*CAAPIPAQAAPG GHRAAG*SRRGTPAR*SARAPRGFRTPPAPPG*CAESRRRAAQRSRRGGHSGKCW*RPRP PARRRLPAAASTGAPNNRCGSAARPGRR*PPPAG*GPAPATRAGCRAASWRSWERSPAHA GGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFRDARRQAAVVVLALHPDRPLWRVDVD VVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGGDGRVLREETMAGLDEGPAGGRIDAG EVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAVAVATGDGAIQLGGAGAHHGGEDHVG ARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQVAHHMVAFPRIDVVRADEHHPLAVV ANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVAEQRVGALDHRHHRLARVRHVAAHEE PYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADAALAVQLLDREQCAIRVRALDIGGDA GFGEQQADQRPLLVRSHPFPLL*LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPA VP |
>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR*SACCSP KPASPPISSARTRMAHCSRSSN*TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGG YGSSWAATCRTRARR*CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT* FATTASGWCSSARTTSIRGKATM*CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTR RAPTWSSPPWWAPAPPSCIAPSPVATATAGGRRSPA*PPARRRWRRWRVTWQRGRWWSRL TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG PPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRPGLAADPHRLFGAPVLAAAGSLRR AGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGVRKPRGALADHRAGVPRRDHPAAR CPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGPDQPGQGVADAAPWLGRARGAPAP VAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ*QEGYRHHAGTGSAVRWRGAVSQCRL VAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSRAGLAEGRSADPAIRFYLSVGGRQPV PRX >X13776_2 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLR NRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNAVPGPRRRPGPLSAVRRGLHSQPGG TVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAEPEQCAAGGVPD SPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGARGNLHSAVSLRRRLAARRRAHLPG ARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQPDHQRGGGGEDGE*RGRGAGGGRAL LLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQLAGGRRAAAPV RHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRPLCRRA*PRRLV RQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV PVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLD AHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHL SREAMKRREPILKIAQELLGNEPSA*AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVW LLGKISGREVAVINFLVGVLSACVAFYLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQF LE >X13776_3 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY DIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWS ASMGGGPLP*APTRCSAACASCRCWSSTRRGRSATPWSCS*SASVVRCASAGRRRKPSTC RWTWSSPAFSRMATTTRSLRCSPPGLRALPWWRWWSTKAPRCSRRSSSWSATA*SPSRSM PTGCCLCWYRRGASARKWRS*SRRPSSSRTASPARPGSTRPRCC*CSAMAGTSARRTSTC RGKR*SGASRS*RSLRSCWETSRPPERSGPTRTITRGVSSSCWDWFCCTLARCCFSMPSG CWARSAVGRWR*STSWSAC*APASRST*SFPQQPGRAR*RPER*PCYSLLPICGWPPTSS SX >X13776_4 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation SRNWLAATHR*VKANSRVSAPAFSEPCPAAAEKIR*NATQALSTPTRKLITATSRPLILP SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS*AIFRIGSRRFIAS RDRCWCASRSSQPWRCISNTLAWLIRAWPAMRSWSCSVFCFSFAISSLMRRADTSTGSTR WASSGWVITPWHSSSMICESTAGLSYSTSATRVVRGVPAASSAAISSWWPFWKMLVKTTS TGTSKASGGGQHWRTEQPMRISCKTRASLTSPGGLRTSTCNSRRLPSSELALMGAVPRPC WRTSRRGYARRHKGRGESVRATASGPGTRRAHRFPRCAKTGGCGCSGAPPGPAPVARRCR CRTGAAARLPPASCLRPARRGRATRSASRPPRPRR*WSRSPGRNHGRPGRRPGWRAYRCW RSKARPPPAPLPRHSPSSPPPPRWWSGWRSAAACRRRSDGRWRDTARRCRCPPRWRRPRR RAPGRCARRRAASRRRRDTAECRFPRAPCRRAGDTGGASHGCFPADRCSPSR*TPPARRS GESGTPPAAHCSGSAPDRRRRCSANTRSPRRGSGSRAARRRARPPASPPCACATCSSPRG TVPPGCE*SPRRTADSGPGRRRGPGTAFRSGDRRRRPRGSVARPRAMRHTRASARYRR*R RFRRTAGRSAAAPGAIPSVSSPVTVAQRRTKRTRSCSRLAR*IVQFPSPGWW*SSRCSAS GT >X13776_5 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation LEELVGGHPQIGKSE*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA QQPDGIEKQHRANVQQNQSQHDDDTPLVIVLVGPDRSGGRLVSQQLLSDLQDRLAPLHRF PRQVLVRLALVPAMALHQQHLGLVDPGLAGDAVLELLGLLLQLRHFLADAPRRYQHRQHP VGIERLGDHAVALQLDDLREHRGAFVLHQRHQGSARSPGGEQRSDLVVVAILENAGEDHV HRHVEGFRRRPALAHRTTDADQLQDQGVADLPRRVEDQHLQLAQAAEQRVGAHGSGPPPM LADQSSRLCTTT*GSGRIGSGDCQRTWNTPRASISAMREDRRLWLFWRSTRTGPCGASMS MSYRCRCTSSTRQLPAACAARPSNKVCQ*AASAQAVMVAFSGKKPWQAWTKARLAGVSML EK*GATTTCPSATSLSIFATSASLVVRLAIGGRLPSP*RRAMARYSSAVPVPTTVEKTTS ARAW*MRSTARCKSSSEGYSGM*ISSSTVPPCWRYRWRITWLLSRG*M*SEPMNTTRSP* WRIRYAASGALFWFGAGPP*TMFGEYSKPS*GVG*QSSASARSTTGITALRVCDM*QPTR NRTPRLRMKSSAHSR*RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVT PVSENSRPISGRSWCDPIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQ RYX >X13776_6 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation RGTGWRPPTDR*KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS*SPPPPDR*SCP ATRRH*ETAPRQRTAEPVPA**RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLP ATGAGAPRARPSHGAASATPWPG*SGPGRRCGPGAARSSASASPFPR*CAAPIPAQAAPG GHRAAG*SRRGTPAR*SARAPRGFRTPPAPPG*CAESRRRAAQRSRRGGHSGKCW*RPRP PARRRLPAAASTGAPNNRCGSAARPGRR*PPPAG*GPAPATRAGCRAASWRSWERSPAHA GGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFRDARRQAAVVVLALHPDRPLWRVDVD VVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGGDGRVLREETMAGLDEGPAGGRIDAG EVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAVAVATGDGAIQLGGAGAHHGGEDHVG ARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQVAHHMVAFPRIDVVRADEHHPLAVV ANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVAEQRVGALDHRHHRLARVRHVAAHEE PYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADAALAVQLLDREQCAIRVRALDIGGDA GFGEQQADQRPLLVRSHPFPLL*LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPA VP |
>X13776_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation VPLAEHLLDHHQPGEASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLRNRRHRRY VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE X |
>NC_001321.1_1 Balaenoptera physalus mitochondrion, complete genome VNY*SAHDHNMTEVSYIWYFFIFFGGLARTPLWP**VSSQSDKL*LGLDVFVIWLAQPTC AVKLMVTGHSTPLFPPGSKNCMS**TKPPSFHTMLTLCLDIHHPP*QARP*I*KPFYL*I NTKSDTSPMMKMHERHPYPMRWCSLNTYKA*HWKCLDGSSQPHWH**FGPSLSISS*QTY TCKYPHPSENAL*IMKIK*SGYQAR*H*QLTTPRLATPPRDTAVMKIKL*TKVRLSHVNL *VGKLRASHRGHTIDPN**KHGVKSVKEPHEMKSNLN*AVKSPN*N*AKLRKWL*YNLIT RQL*SKLGLDTPLCLVVNPNSHKT*LFA*VLLATA*NSKDLAVPHTHLEEPVL*PMNPDQ PHQPLLLQSMYRHLQQTLKGEK*A*PSYMKTLGQGVTHGLGSNGLHFLS*EHPLYSHESF YET*KLKEDLVVNQEQSAWLNKAM*ARTHRPSPSSSTPAMNPSSLTQAKQLYE**QVVT* *AYRKVCLDKT*YSLNKACSLHLEDSTARVYLELALAHTLPTSTTTNQSNKTFTIPSKY* **KFKYQWRY*DSTV*KDE*KT*K**KAKLTTCTFCMMT*LVMN*Q*DLKLNYPKPDELL MSST*NELIYVAK*WEDL*VEVKSLTSLVMAGCPWKESQFNIK*Y*KPMPSLNVYLTVNL K*YSFLEMGTTLT*E*NQT*T*LA*KQPSIKKAFKLDNKMMF*FQH*VNQLLAWLLD*SM QM*KQYC*YE*QEIFLLAQAYTSNW*YTDN*QQMNKTQH*IIY*NTVNPTQACIKE*LKK VKGTRQTQTPPVYQKHHL*HNQY*STACPVTNR*TAAVSWPCKGSMITCSLI*DLYEWPH EGFTVSYF*SVKLTSPW*GGDNKM*REDPMELQLINPKTMTLNHQGMTKPYMGWQFRLGW PRSTKNPPSD*NLGPLAKVQYHLLIQSFDQRNKLP*G*QRNPILESMSTMGFTTSMLDQD ILMVQLLL*VRLFND*SPTWSEF*PE*S*SVSIYYAFLPVRKDK*NKANFKQAPSNN*WP SLNLMIKRKQTCP*PGPCWGG*VR*LHKT*TFTP*GSNPLPNKMFMINILTLILPILLAV AFLTLVERKILGYMQFRKGPNIVGPHGLLQPFADAIKLFTKEPLRPATSSTTMFIIAPVL ALTLALTMWSPLPMPYPLINMNLGVLFMLAMSSLAVYSILWSGWASNSKYALIGALRAVA QTISYEVTLAIILLSVLLMNGSYTLSTLATTQEQLWLLFPSWPLAMMWFISTLAETNRAP FDLTEGESELVSGFNVEYAAGPFALFFLAEYANIIMMNMLTAILFLGTFHNPHNPELYTA NLIIKTLLLTMSFLWIRASYPRFRYDQLMHLLWKNFLPLTLALCMWHISLPIMTASIPPQ T*EMCLMKELLW*SK***PKSSYF*NN*NRTYP*EFKVLRATMLHYNLQ*GQLNKLSGPY PENVGSYPSHTNKPINPYYPPDNPYP*YNNGSHQLSLTISLNWLRNEHNSLHPYHNKKSY SPGH*SFYQVPPNTSHCFRTPHNSSHH*LNAL*PMNYYKTI*PNSIHTHNSSPSHQTGIS PLPLLSS*SNT*YPPNH*PNPINMTKTSSLINPMPNFTIN*PTPNINHILTFHLN**L*W TKPNTTSKNHSLLINCPH*MNNGHSTM*SNPNITKSTNLHHNNLHHIYIIYPKLNYHYIV TVSNLK*NTRHHNPYHTHFTLD**TPTTIGVYTQMNNYS*TNKKWYTHCTNIHSHYSITQ PMLLYTSYLLHSTNTISLHK*YKNKMTIQLHKTNSSPTNSNRNFHYATTPHTNTLNPTMG V*VKP*P*AFKALSKYNLLNSCPM*TA*LYLTSIECKSNALIKLNPH*IGGMHLPRIFS* QLNTLINWLQSTSPAA*KK*REKSRQDLKLLPWICNSKWSFTTGLGKK*TQPLSLDLQSN TYSAILPMFMNRWLFSTNHKDIGTLYLLFGAWAGMVGTGLSLLIRAELGQPGTLIGDDQV YNVLVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLM ASSMIEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKP PAMTQYQTPLFVWSVLVTAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQH LFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMVSIGFLGFIVWAHHMF TVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPALMWALGFIFLFTVGGL TGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNTTWAKIH FMIMFVGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNTISSMGSFISLTAVMLMIFIIW EAFTSKREVLAVDLTSTNLEWLNGCPPPYHTFEEPAFVNPKWS*KEGIEPSPIGFKPTS* LLCLSL*T*Y**NLM*LCQS*VTSENPVYLHGMSIPT*FP*CSITHH**APTLSRSYTNN RFSN*LFSSLHYYPNAYNQINTY*YN*RP*S*NCLNYPPSHYLNFNCLAFITDPLHN*RS Q*PLPHCKNN*SPMMLKLWVYRLR*PKLRLLYNPNI*PKA**TTII*S**PSCLTY*NNN PNISLI**RTPLMGRTLLGPKN*CNP*TPKPNNLNINTT*PILWTML*DLRLKPQFHTNC P*TSTP*SLWKMICINTMTSL*S*ISINLLS**L*VYNSP*WYATI*YINMTPYYSINTL NPLCIIPIKNLKALLFP*PQTSTYQNTKTTSSLKHHMNENLFAPFMIPVMLGIPITTLII ILPSMLFPAPNRLINNRTIAIQQWLTKLTSKQLMNVHSPKGQTWSLMLISLFLFIASTNL LGMLPHSFTPTTQLSMNVGMAIPLWAGTVTTGFRNKTKMSLAHLLPQGTPTFLIPMLVII ETISLFIQPVAWAVRLTANITAGHLLMHLIGETTLALMNINLFSAFITFTILALLTILEF AVALIQAYVFTLLVSLYLHDNT*WPTKPTHTT**TPALDPSPELYQPF**HQA*LYDFTS TQYSY*L*ACQQMF*QYTNDGEMSSEKAPSKAIMHQPSK*AYDTE*FYLSSQKSYFSQAS SEPSTTQALPLLQN*ADVDHQQASAL*IP*KFPFSTPPYY*PLAYLLPEPTMAW*KETAN TYFKHSSSQLH*ASTSPYYKHQSTTKPLSQSQTESTAPPSL*PQAFMGYM*SLDLLSLSS VSYVK*NSTSHQTTTLALNVPLDTDIS*TSYDYFFMYLSIDEVPSPFSINKYNWLPIS*F RCTPKKNNKPSTNTTNKYNTSPTTRIHRLLTSTTKRMR*KNKPMWMRIWPH*ISPPTLLH KILLGGHYFPSLWL*NRSLTPPSLSNSVKQPKHNTHNSLILNLPTSSQPSLWMNS**P*M SWMWYLV*DKTSDFDPLDCDQIHNYQMTLIHMNILMAFSMSLMGLLMYRSHLMSALLCLE GMMLSLFVLAALTILSSHFTLANMMPIILLVFAACEAAIGLALLVMVSNTYGTDYVQNLN LLQC*NLLFLQSY*YP*PDYQKMT*SELTPQPTVY*LASQAFSSSINSTTTALTTH*YSS PTPFLPHSWS*QYDSFP*Y**QVNPISSKNHQSEKNSTLRY*SHYKPS*L*HLLPLN*SY FMSYLKPH*SLPLSLSLAGATKQNDSMPDYTSYSMH*LDLSHY**H*YIYKMQQDP*TFY SYNTELNHYLRPDPTSSYD*PA**PS**KYLSMDYTFDCPKHT*KPPLQAP*SLQPYY*N LEAMAYYELHPYSIP*QNT*HTHFLYSLFEE*S*PALSVYVKQT*NH*LHIPQLVT*HSS SQLSSSKPPEAM*GPLP**LPTASHPPYYSVWQTRTTNAFMAEP*FCPEAYKSFYH**PV DDY*QA*QILHYPQPST*SENYS*SCRSSHDQIPLFS**EQML*LLLSTLYMY*S*HNVA NTHTTSMMSPLPSHESMP**PYTLFPSCSYH*TLKSS*ALSTVSMV*K*R*FVKLTMEDQ NFLLTEKVLQELLIHAPTPNSCGFFKLLQDSSYPLVLGAKKLVQLQMKVMNLFTSFTLLT LLILTTPIMMSHTGSHVNNKYQSYVKNIVFCAFITSLVPAMVYLHTNQETLISNWHWITI QTLKLTLSFKMDYFSLMFMPVALFITWSIMEFSMWYMHSDPYINQFFKYLLLFLITMLIL VTANNLFQLFIGWEGVGIMSFLLIGWWFGRTDANTAALQAILYNRIGDIGLLASMAWFLS NMNTWDLEQIFMLNQNPLNFPLMGLVLAAAGKSAQFGLHPWLPSAMEGPTPVSALLHSST MVVAGIFLLVRFYPLMENNKLIQTVTLCLGAITTLFTAICALTQNDIKKIIAFSTSSQLG LMMVTIGLNQPYLAFLHICTHAFFKAMLFLCSGSIIHNLNNEQDIRKMGGLFKALPFTTT ALIIGCLALTGMPFLTGFYSKDPIIEAATSSYTNAWALLLTLIATSLTAVYSTRIIFFAL LGQPRFPPSTTINENNPLLINPIKRLLVGSIFAGFILSNSIPPMTTPLMTMPLHLKLTAL AMTTLGFIIAFEINLDTQNLKHKHPSNSFKFSTLLGYFPTIMHRLPPHLDLLMSQKLATS LLDLTWLETILPKTTALIQLKASTLTSNQQGLIKLYFLSFLITITLSMILFNYPE*SP** LQH**MKTNP*QSPTKHHNYMMPQSL*PPH*KPQNPQYHKQPSPLVHQTQT*SSPPHSSK HKSQLKTPPPTLKQMLLVQLY*KPKPQDTVQ*P*LLYNQMLPAFPPNKSKTPLTPKTNHQ NSK*LHIQHHHPQSTLNPHK*VKALKKPPQN*LQK*YLKWKQYTLSLFSHGLQPWPMTWK IIVVIQLQEHQWPTSEKHTH**KSSTTHSSISPPHQMSLHDGTSAPYSASA*LYKS*QAY S*QYTTHQTQQPPSHQSHTSAETWITAELSDTYMQMGLLYSSSASTLT*DEAYTTAPTPS EKHEMLELFYYSQL*PPHS*ATSCPEDKYHSEAQL*SLTSYQQSHTLVPP*SNESEAVSL *MKQH*HAFLPFTLSSPSSS*H*QLSTLFSFTKQDPTTPQASHPT*MKSHSTPTTQLKTF *VPYY*S*SY*Y*PYSHPTYLETQTTMPQQTHSVPQHTLNQNGIFYSHTQSYDQSPTN*A ES*PYYSQS*S*PSSQYSTHPINEA*YFDPLASSCSES*SQIY*P*HGSAANQ*NTPT*L *ANSHPSSISS*F*Y*YQ*LVLS*TNL*NEESL*YN*MPRFCKPEKET*HTSL*LKEEVL HSTISTQSWSST*TIPWKSMLYNNH*TTVLCPYWK*LALLDIIM*LVHACTST*LMASFH GYEQMYMLCMIVHSIIFTTSSWSSY*ILLILHIT*YVLMVQ*RMFLCIP*SI*IKWFLWP LH*ITSLVSMPRETSNPLG*DPSSRTGPITRGGSYLMIFM*HLVLTSGPY*LKIAHSFPL NKTSRW |
One or more peptide sequences are written out.
The names of the resulting protein sequences are formed from the name of the input nucleic acid sequence with '_' and the translation frame appended to it. Thus a nucleic acid sequence with the name 'XYZ' franslated in all 6 frame would produce protein sequences with the names: 'XYZ_1', 'XYZ_2', 'XYZ_3', 'XYZ_4', 'XYZ_5', 'XYZ_6'.
If regions are specified, they are taken to be translated in frame 1 and so the output name would be 'XYZ_1'.
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 EMBOSS REBASE restriction enzyme data files are stored in directory 'data/REBASE/*' under the EMBOSS installation directory.
These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager.
The data files are stored in the REBASE directory of the standard EMBOSS data directory. The names are:
The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype, if you wish.
The format of the file "embossre.equ" is
Enzyme-name Prototype-name
i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred (prototype) name.
Termination (STOP) codons are translated as the character *. The -trim option removes all all X and * characters from the right end of the translation. This trimming process starts at the end and continues until the next character is not an X or a *. The -clean option changes all STOP codon positions from the * character to X (an unknown residue). This is useful because some programs will not accept protein sequences with * characters in them.
The reverse frame '-1' is defined as the translation you get when you use the reverse-complement of the sequence with the same codon phase as the codon in frame '1'. Thus the sequence ACTGG in frame 1 is the translation of the codons ACT,GG; the translation of frame -1 uses these same codons, reverse complemented: forward sense ACT GG reverse sense TGA CC reverse-complement CC AGT frame -1 translation S
Frame -1 is the translation of CCAGT (the reverse complement of ACTGG) using the codon AGT (the first bases CC are ignored). The result is the peptide S.
Similarly frame -2 is the phase used by frame 2, CAG T (the first base C is ignored). The last base cannot be successfully translated and is output as the unknown residue X. The result is the peptide QX.
Frame -3 is the phase used by frame 3, CCA GT. The last two bases will translate to V as it does not matter what the next base is. (GTA, GTC, GTG, GTT all code for V). The result is the peptide PV.
The alternative way of generating the reverse translation frames used by some people is that frame -1 is made by taking the frame '1' of the reverse complement. There is no correspondence between the codons used in frame 1 and -1, 2 and -2, 3 and -3; the codons used change with the length modulus 3.
There does not appear to be a convention on which definition to use. The Staden package uses the same convention as this program. The GCG package sneakily avoids the problem by naming the frames using letters (a, b, c, d, e, f). If you really need to define frame -1 as the frame given when you reverse complement the sequence and then start translating at the first frame in the resulting sequence, then use the -alternative qualifier.
When translating using a non-standard genetic code, you should check the table carefully for deviations from your particular organism's code.
When using the -regions option, you should always leave the -frames option at the default of frame '1'. If you change the frame while specifying a region to translate, then the regions will be offset by 1 or 2 bases, which is not what you want.
Program name | Description |
---|---|
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 |
coderet | Extract CDS, mRNA and translations from feature tables |
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 |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
June 2002 - added '-alternative' qualifier - Gary Williams