transeq.txt

emboss的linux版本的源代码

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 regul
ation
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
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'.

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 column information is described at the top of the data files

   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 translating 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
   backtranambig Back translate a protein sequence to ambiguous codons
   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