dotmatcher.input

emboss的linux版本的源代码

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

'tsw:hba_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:hba_human</h3>
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<pre>
ID   HBA_HUMAN      STANDARD;      PRT;   141 AA.
AC   P01922;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   HEMOGLOBIN ALPHA CHAIN.
GN   HBA1 AND HBA2.
OS   Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS   Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE FROM N.A. (ALPHA-1).
RX   MEDLINE; 81088339.
RA   MICHELSON A.M., ORKIN S.H.;
RT   "The 3' untranslated regions of the duplicated human alpha-globin
RT   genes are unexpectedly divergent.";
RL   Cell 22:371-377(1980).
RN   [2]
RP   SEQUENCE FROM N.A. (ALPHA-2).
RX   MEDLINE; 81175088.
RA   LIEBHABER S.A., GOOSSENS M.J., KAN Y.W.;
RT   "Cloning and complete nucleotide sequence of human 5'-alpha-globin
RT   gene.";
RL   Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).
RN   [3]
RP   SEQUENCE FROM N.A. (ALPHA-2).
RX   MEDLINE; 80137531.
RA   WILSON J.T., WILSON L.B., REDDY V.B., CAVALLESCO C., GHOSH P.K.,
RA   DERIEL J.K., FORGET B.G., WEISSMAN S.M.;
RT   "Nucleotide sequence of the coding portion of human alpha globin
RT   messenger RNA.";
RL   J. Biol. Chem. 255:2807-2815(1980).
RN   [4]
RP   SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2).
RA   FLINT J., HIGGS D.R.;
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   SEQUENCE.
RA   BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA   RUDLOFF V., WITTMANN-LIEBOLD B.;
RT   "The constitution of normal adult human haemoglobin.";
RL   Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN   [6]
RP   SEQUENCE.
RA   HILL R.J., KONIGSBERG W.;
RT   "The structure of human hemoglobin: IV. The chymotryptic digestion of
RT   the alpha chain of human hemoglobin.";
RL   J. Biol. Chem. 237:3151-3156(1962).
RN   [7]


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

FT                                /FTId=VAR_002841.
FT   VARIANT     130    130       A -&gt; D (IN YUDA; O2 AFFINITY DOWN).
FT                                /FTId=VAR_002842.
FT   VARIANT     131    131       S -&gt; P (IN QUESTEMBERT; HIGHLY UNSTABLE;
FT                                CAUSES ALPHA-THALASSEMIA).
FT                                /FTId=VAR_002843.
FT   VARIANT     133    133       S -&gt; R (IN VAL DE MARNE; O2 AFFINITY UP).
FT                                /FTId=VAR_002844.
FT   VARIANT     135    135       V -&gt; E (IN PAVIE).
FT                                /FTId=VAR_002845.
FT   VARIANT     136    136       L -&gt; M (IN CHICAGO).
FT                                /FTId=VAR_002846.
FT   VARIANT     136    136       L -&gt; P (IN BIBBA; UNSTABLE;
FT                                CAUSES ALPHA-THALASSEMIA).
FT                                /FTId=VAR_002847.
FT   VARIANT     138    138       S -&gt; P (IN ATTLEBORO; O2 AFFINITY UP).
FT                                /FTId=VAR_002848.
FT   VARIANT     139    139       K -&gt; E (IN HANAKAMI; O2 AFFINITY UP).
FT                                /FTId=VAR_002849.
FT   VARIANT     139    139       K -&gt; T (IN TOKONAME; O2 AFFINITY UP).
FT                                /FTId=VAR_002850.
FT   VARIANT     140    140       Y -&gt; H (IN ROUEN; O2 AFFINITY UP).
FT                                /FTId=VAR_002851.
FT   VARIANT     141    141       R -&gt; C (IN NUNOBIKI; O2 AFFINITY UP).
FT                                /FTId=VAR_002852.
FT   VARIANT     141    141       R -&gt; L (IN LEGNANO; O2 AFFINITY UP).
FT                                /FTId=VAR_002853.
FT   VARIANT     141    141       R -&gt; H (IN SURESNES; O2 AFFINITY UP).
FT                                /FTId=VAR_002854.
FT   VARIANT     141    141       R -&gt; P (IN SINGAPORE).
FT                                /FTId=VAR_002855.
FT   HELIX         4     35
FT   HELIX        37     42
FT   TURN         44     45
FT   TURN         50     51
FT   HELIX        53     71
FT   TURN         72     74
FT   HELIX        76     79
FT   TURN         80     80
FT   HELIX        81     89
FT   TURN         90     91
FT   TURN         95     95
FT   HELIX        96    112
FT   TURN        114    116
FT   HELIX       119    136
FT   TURN        137    139
SQ   SEQUENCE   141 AA;  15126 MW;  5EC7DB1E CRC32;
     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
     VHASLDKFLA SVSTVLTSKY R
//
</pre>
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<p><h3>Database entry: tsw:hbb_human</h3>
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<pre>
ID   HBB_HUMAN      STANDARD;      PRT;   146 AA.
AC   P02023;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   HEMOGLOBIN BETA CHAIN.
GN   HBB.
OS   Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS   Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE.
RC   SPECIES=HUMAN;
RA   BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA   RUDLOFF V., WITTMANN-LIEBOLD B.;
RT   "The constitution of normal adult human haemoglobin.";
RL   Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 81064667.
RA   LAWN R.M., EFSTRATIADIS A., O'CONNELL C., MANIATIS T.;
RT   "The nucleotide sequence of the human beta-globin gene.";
RL   Cell 21:647-651(1980).
RN   [3]
RP   SEQUENCE OF 121-146 FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 85205333.
RA   LANG K.M., SPRITZ R.A.;
RT   "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT   segments.";
RL   Gene 33:191-196(1985).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC   SPECIES=HUMAN;
RX   MEDLINE; 76027820.
RA   FERMI G.;
RT   "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT   2.5-A resolution: refinement of the atomic model.";
RL   J. Mol. Biol. 97:237-256(1975).
RN   [5]
RP   SEQUENCE.
RC   SPECIES=P.TROGLODYTES;
RX   MEDLINE; 66071496.
RA   RIFKIN D.B., KONIGSBERG W.;
RT   "The characterization of the tryptic peptides from the hemoglobin of
RT   the chimpanzee (Pan troglodytes).";
RL   Biochim. Biophys. Acta 104:457-461(1965).
RN   [6]


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

FT   VARIANT     140    140       A -&gt; T (IN ST JACQUES: O2 AFFINITY UP).
FT                                /FTId=VAR_003081.
FT   VARIANT     140    140       A -&gt; V (IN PUTTELANGE; POLYCYTHEMIA;
FT                                O2 AFFINITY UP).
FT                                /FTId=VAR_003082.
FT   VARIANT     141    141       L -&gt; R (IN OLMSTED; UNSTABLE).
FT                                /FTId=VAR_003083.
FT   VARIANT     142    142       A -&gt; D (IN OHIO; O2 AFFINITY UP).
FT                                /FTId=VAR_003084.
FT   VARIANT     143    143       H -&gt; D (IN RANCHO MIRAGE).
FT                                /FTId=VAR_003085.
FT   VARIANT     143    143       H -&gt; Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT                                /FTId=VAR_003086.
FT   VARIANT     143    143       H -&gt; P (IN SYRACUSE; O2 AFFINITY UP).
FT                                /FTId=VAR_003087.
FT   VARIANT     143    143       H -&gt; R (IN ABRUZZO; O2 AFFINITY UP).
FT                                /FTId=VAR_003088.
FT   VARIANT     144    144       K -&gt; E (IN MITO; O2 AFFINITY UP).
FT                                /FTId=VAR_003089.
FT   VARIANT     145    145       Y -&gt; C (IN RAINIER; O2 AFFINITY UP).
FT                                /FTId=VAR_003090.
FT   VARIANT     145    145       Y -&gt; H (IN BETHESDA; O2 AFFINITY UP).
FT                                /FTId=VAR_003091.
FT   VARIANT     146    146       H -&gt; D (IN HIROSHIMA; O2 AFFINITY UP).
FT                                /FTId=VAR_003092.
FT   VARIANT     146    146       H -&gt; L (IN COWTOWN; O2 AFFINITY UP).
FT                                /FTId=VAR_003093.
FT   VARIANT     146    146       H -&gt; P (IN YORK; O2 AFFINITY UP).
FT                                /FTId=VAR_003094.
FT   VARIANT     146    146       H -&gt; Q (IN KODAIRA; O2 AFFINITY UP).
FT                                /FTId=VAR_003095.
FT   HELIX         5     15
FT   TURN         16     17
FT   HELIX        20     34
FT   HELIX        36     41
FT   HELIX        43     45
FT   HELIX        51     55
FT   TURN         56     56
FT   HELIX        58     75
FT   TURN         76     77
FT   HELIX        78     94
FT   TURN         95     96
FT   TURN        100    100
FT   HELIX       101    121
FT   HELIX       124    142
FT   TURN        143    144
SQ   SEQUENCE   146 AA;  15867 MW;  EC9744C9 CRC32;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
//
</pre>
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