infoalign.input

emboss的linux版本的源代码

<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: globins.msf</h3>
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<pre>
!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~

</pre>
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<a name="input.8"></a>
<h3>Input files for usage example 8</h3>

'tembl:eclac*' is a sequence entry in the example nucleic acid database 'tembl'
<p>

<a name="input.9"></a>
<h3>Input files for usage example 9</h3>
<p><h3>Database entry: tembl:eclacz</h3>
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<pre>
ID   ECLACZ     standard; DNA; PRO; 3078 BP.
XX
AC   V00296;
XX
SV   V00296.1
XX
DT   13-JUL-1983 (Rel. 03, Created)
DT   06-MAR-1996 (Rel. 47, Last updated, Version 4)
XX
DE   E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW   galactosidase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RP   1-3078
RX   MEDLINE; 84028567.
RA   Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT   "Sequence of the lacZ gene of Escherichia coli";
RL   EMBO J. 2:593-597(1983).
XX
RN   [2]
RX   MEDLINE; 87275876.
RA   Zell R., Fritz H.J.;
RT   "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT   deamination of 5-methyl-cytosine residues";
RL   EMBO J. 6:1809-1815(1987).
XX
DR   SWISS-PROT; P00722; BGAL_ECOLI.
XX
CC   Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..3078
FT                   /db_xref="taxon:562"
FT                   /organism="Escherichia coli"
FT   CDS             &lt;1..3072
FT                   /db_xref="SWISS-PROT:P00722"
FT                   /note="galactosidase"
FT                   /transl_table=11
FT                   /protein_id="CAA23573.1"
FT                   /translation="TMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTD
FT                   RPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVT
FT                   YPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQ
FT                   DSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQI
FT                   SDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDE


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

     gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt       180
     gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag       240
     gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac       300
     accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg       360
     ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga       420
     attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt       480
     tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga       540
     gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag       600
     gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca       660
     caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg       720
     gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta       780
     tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat       840
     gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg       900
     tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc       960
     acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt      1020
     ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat      1080
     cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag      1140
     cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg      1200
     ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg      1260
     gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta      1320
     acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat      1380
     gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct      1440
     tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc      1500
     ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc      1560
     aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac      1620
     gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc      1680
     cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa      1740
     aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag      1800
     ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca      1860
     aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc      1920
     gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt      1980
     aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt      2040
     gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta      2100
     gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg      2160
     cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg      2220
     accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc      2280
     cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg      2340
     cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc      2400
     attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca      2460
     gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac      2520
     gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt      2580
     agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg      2640
     cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta      2700
     gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg      2760
     ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg      2820
     acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc      2880
     cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa      2940
     ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc      3000
     ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg      3060
     tgtcaaaaat aataataa                                                    3078
//
</pre>
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