backtranseq.input

emboss的linux版本的源代码

<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:opsd_human</h3>
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<pre>
ID   OPSD_HUMAN     STANDARD;      PRT;   348 AA.
AC   P08100; Q16414;
DT   01-AUG-1988 (Rel. 08, Created)
DT   01-AUG-1988 (Rel. 08, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   RHODOPSIN.
GN   RHO.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 84272729.
RA   NATHANS J., HOGNESS D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   SEQUENCE OF 1-120 FROM N.A.
RA   BENNETT J., BELLER B., SUN D., KARIKO K.;
RL   Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   REVIEW ON ADRP VARIANTS.
RX   MEDLINE; 94004905.
RA   AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
RA   BHATTACHARYA S.;
RT   "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
RL   Hum. Mutat. 2:249-255(1993).
RN   [4]
RP   VARIANT ADRP HIS-23.
RX   MEDLINE; 90136922.
RA   DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
RA   YANDELL D.W., SANDBERG M.A., BERSON E.L.;
RT   "A point mutation of the rhodopsin gene in one form of retinitis
RT   pigmentosa.";
RL   Nature 343:364-366(1990).
RN   [5]
RP   VARIANTS ADRP.
RX   MEDLINE; 91051574.
RA   FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
RA   HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
RA   WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
RA   BHATTACHARYA S.S., HUMPHRIES P.;
RT   "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
RT   proline--&gt;histidine substitution (codon 23) in pedigrees from
RT   Europe.";
RL   Am. J. Hum. Genet. 47:941-945(1990).
RN   [6]
RP   VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
RX   MEDLINE; 91015273.


<font color=red>  [Part of this file has been deleted for brevity]</font>

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -&gt; M (EFFECT NOT KNOWN).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -&gt; P (IN ADRP).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -&gt; R (IN ADRP).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -&gt; K (IN ADRP).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -&gt; C (IN ADRP).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -&gt; R (IN ADRP).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       MISSING (IN ADRP).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       MISSING (IN ADRP).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -&gt; L (IN ADRP).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -&gt; R (IN ADRP).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -&gt; E (IN CSNB4).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -&gt; E (IN ADRP).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -&gt; R (IN ADRP).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -&gt; M (IN ADRP).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -&gt; L (IN ADRP).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -&gt; M (IN ADRP).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -&gt; A (IN ADRP).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -&gt; L (IN ADRP; COMMON VARIANT).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -&gt; Q (IN ADRP).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -&gt; R (IN ADRP).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -&gt; S (IN ADRP).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38892 MW;  07443BEA CRC32;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
</pre>
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<a name="input.2"></a>
<h3>Input files for usage example 2</h3>
<p><h3>Database entry: tsw:ach2_drome</h3>
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<pre>
ID   ACH2_DROME     STANDARD;      PRT;   576 AA.
AC   P17644;
DT   01-AUG-1990 (REL. 15, CREATED)
DT   01-AUG-1990 (REL. 15, LAST SEQUENCE UPDATE)
DT   01-NOV-1997 (REL. 35, LAST ANNOTATION UPDATE)
DE   ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-LIKE CHAIN 2 PRECURSOR.
GN   ACRE OR SAD OR ACR96AB.
OS   DROSOPHILA MELANOGASTER (FRUIT FLY).
OC   EUKARYOTA; METAZOA; ARTHROPODA; TRACHEATA; HEXAPODA; INSECTA;
OC   PTERYGOTA; DIPTERA; BRACHYCERA; MUSCOMORPHA; EPHYDROIDEA;
OC   DROSOPHILIDAE; DROSOPHILA.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   TISSUE=HEAD;
RX   MEDLINE; 90301489.
RA   BAUMANN A., JONAS P., GUNDELFINGER E.D.;
RT   "Sequence of D alpha 2, a novel alpha-like subunit of Drosophila
RT   nicotinic acetylcholine receptors.";
RL   NUCLEIC ACIDS RES. 18:3640-3640(1990).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   TISSUE=HEAD;
RX   MEDLINE; 90353591.
RA   JONAS P., BAUMANN A., MERZ B., GUNDELFINGER E.D.;
RT   "Structure and developmental expression of the D alpha 2 gene
RT   encoding a novel nicotinic acetylcholine receptor protein of
RT   Drosophila melanogaster.";
RL   FEBS LETT. 269:264-268(1990).
RN   [3]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 90360975.
RA   SAWRUK E., SCHLOSS P., BETZ H., SCHMITT B.;
RT   "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD,
RT   a novel developmentally regulated alpha-subunit.";
RL   EMBO J. 9:2671-2677(1990).
CC   -!- FUNCTION: AFTER BINDING ACETYLCHOLINE, THE ACHR RESPONDS BY AN
CC       EXTENSIVE CHANGE IN CONFORMATION THAT AFFECTS ALL SUBUNITS AND
CC       LEADS TO OPENING OF AN ION-CONDUCTING CHANNEL ACROSS THE PLASMA
CC       MEMBRANE.
CC   -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC   -!- TISSUE SPECIFICITY: CNS IN EMBRYOS.
CC   -!- DEVELOPMENTAL STAGE: LATE EMBRYONIC AND LATE PUPAL STAGES.
CC   -!- SIMILARITY: BELONGS TO THE LIGAND-GATED IONIC CHANNELS FAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to [e-mail]).
CC   --------------------------------------------------------------------------
DR   EMBL; X52274; G7803; -.
DR   EMBL; X53583; G8533; -.
DR   PIR; S11679; ACFFA2.
DR   FLYBASE; FBgn0000039; nAcR-alpha-96Ab.
DR   PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
DR   PFAM; PF00065; neur_chan; 1.
KW   RECEPTOR; POSTSYNAPTIC MEMBRANE; IONIC CHANNEL; GLYCOPROTEIN; SIGNAL;
KW   TRANSMEMBRANE; MULTIGENE FAMILY.
FT   SIGNAL        1     41       PROBABLE.
FT   CHAIN        42    576       ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2.
FT   DOMAIN       42    261       EXTRACELLULAR (POTENTIAL).
FT   TRANSMEM    262    285       POTENTIAL.
FT   TRANSMEM    293    311       POTENTIAL.
FT   TRANSMEM    327    346       POTENTIAL.
FT   DOMAIN      347    526       CYTOPLASMIC (POTENTIAL).
FT   TRANSMEM    527    545       POTENTIAL.
FT   DISULFID    169    183       BY SIMILARITY.
FT   DISULFID    243    244       ASSOCIATED WITH RECEPTOR ACTIVATION
FT                                (BY SIMILARITY).
FT   CARBOHYD     65     65       POTENTIAL.
FT   CARBOHYD    254    254       POTENTIAL.
FT   CARBOHYD    570    570       POTENTIAL.
SQ   SEQUENCE   576 AA;  65506 MW;  7B795689 CRC32;
     MAPGCCTTRP RPIALLAHIW RHCKPLCLLL VLLLLCETVQ ANPDAKRLYD DLLSNYNRLI
     RPVSNNTDTV LVKLGLRLSQ LIDLNLKDQI LTTNVWLEHE WQDHKFKWDP SEYGGVTELY
     VPSEHIWLPD IVLYNNADGE YVVTTMTKAI LHYTGKVVWT PPAIFKSSCE IDVRYFPFDQ
     QTCFMKFGSW TYDGDQIDLK HISQKNDKDN KVEIGIDLRE YYPSVEWDIL GVPAERHEKY
     YPCCAEPYPD IFFNITLRRK TLFYTVNLII PCVGISYLSV LVFYLPADSG EKIALCISIL
     LSQTMFFLLI SEIIPSTSLA LPLLGKYLLF TMLLVGLSVV ITIIILNIHY RKPSTHKMRP
     WIRSFFIKRL PKLLLMRVPK DLLRDLAANK INYGLKFSKT KFGQALMDEM QMNSGGSSPD
     SLRRMQGRVG AGGCNGMHVT TATNRFSGLV GALGGGLSTL SGYNGLPSVL SGLDDSLSDV
     AARKKYPFEL EKAIHNVMFI QHHMQRQDEF NAEDQDWGFV AMVMDRLFLW LFMIASLVGT
     FVILGEAPSL YDDTKAIDVQ LSDVAKQIYN LTEKKN
//
</pre>
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