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transeq |
Function
Translate nucleic acid sequencesDescription
Transeq ranslates nucleic acid sequences to the corresponding peptide sequence.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.
It can translate specified regions 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.
Termination (STOP) codons are translated as the character '*'.
The output peptide sequence is always in the standard one-letter IUPAC code.
Usage
Here is a sample session with transeqTo translate a sequence in the first frame (starting at the first base and proceeding to the end):
% transeq tembl:paamir 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:paamir 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:paamir 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:paamir 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:paamir 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:paamir 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:paamir 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
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence database USA
[-outseq] seqoutall Output sequence(s) USA
Additional (Optional) qualifiers:
-frame menu Frame(s) to translate
-table menu Code to use
-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
-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 '*'
-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.
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.
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outseq" associated qualifiers
-osformat2 string Output seq format
-osextension2 string File name extension
-osname2 string Base file name
-osdirectory2 string Output directory
-osdbname2 string Database name to add
-ossingle2 boolean Separate file for each entry
-oufo2 string UFO features
-offormat2 string Features format
-ofname2 string Features file name
-ofdirectory2 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 standard and additional values
-debug boolean Write debug output to program.dbg
-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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||||||||||||||||||||||||||||
| [-outseq] (Parameter 2) |
Output sequence(s) USA | Writeable sequence(s) | <sequence>.format | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -frame | Frame(s) to translate |
|
1 | ||||||||||||||||||||||||||||||||||||
| -table | Code to use |
|
0 | ||||||||||||||||||||||||||||||||||||
| -regions | 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 | 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 | 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 | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -alternative | 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 | ||||||||||||||||||||||||||||||||||||
Input file format
transeq reads one or more nucleic acid sequence USAs.Input files for usage example
'tembl:paamir' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:paamir
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
//
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Input files for usage example 8
File: mito.seq
>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 |
Output file format
Output files for usage example
File: amir.pep
>PAAMIR_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 |
Output files for usage example 2
File: amir.pep
>PAAMIR_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 |
Output files for usage example 3
File: amir.pep
>PAAMIR_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 |
Output files for usage example 4
File: amir.pep
>PAAMIR_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 >PAAMIR_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 >PAAMIR_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 S |
Output files for usage example 5
File: amir.pep
>PAAMIR_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 >PAAMIR_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 >PAAMIR_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 |
Output files for usage example 6
File: amir.pep
>PAAMIR_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 >PAAMIR_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 >PAAMIR_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 S >PAAMIR_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 >PAAMIR_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 >PAAMIR_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 |
Output files for usage example 7
File: amir.pep
>PAAMIR_1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation VPLAEHLLDHHQPGEASLEHERVRFVRR*ATVTGEETDGIAPGAAADRPAVLRNRRHRRY VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE X |
Output files for usage example 8
File: mito.pep
>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 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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'.
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 EMBOSS REBASE restriction enzyme data files are stored iin 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:
- embossre.enz Cleavage information
- embossre.ref Reference/methylation information
- embossre.sup Supplier information
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.
Notes
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 correspondance betwen 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.
(Reverse sense translations are a biological nonsense, really, but can be very useful in practice.)
References
None.Warnings
When translation using non-standard genetic code table, always 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.
Diagnostic Error Messages
Several warning messages about malformed region specifications:- Non-digit found in region ...
- Unpaired start of a region found in ...
- Non-digit found in region ...
- The start of a pair of region positions must be smaller than the end in ...
Exit status
It exits with status 0, unless a region is badly constructed.Known bugs
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.See also
| Program name | Description |
|---|---|
| backtranseq | Back translate a protein sequence |
| coderet | Extract CDS, mRNA and translations from feature tables |
| plotorf | Plot potential open reading frames |
| prettyseq | Output sequence with translated ranges |
| remap | Display sequence with restriction sites, translation etc |
| showorf | Pretty output of DNA translations |
| showseq | Display a sequence with features, translation etc |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
Author(s)
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
History
Written 4 March 1999 - Gary WilliamsJuly 2001 - changed definition of reverse frames to use the same codon phase as forward frames. - Gary Williams
June 2002 - added '-alternative' qualifier - Gary Williams