est2genome.input

emboss的linux版本的源代码

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

'tembl:hs989235' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:hs989235</h3>
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<pre>
ID   HS989235   standard; RNA; EST; 495 BP.
XX
AC   H45989;
XX
SV   H45989.1
XX
DT   18-NOV-1995 (Rel. 45, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 2)
XX
DE   yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone
DE   IMAGE:177794 3', mRNA sequence.
XX
KW   EST.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-495
RA   Hillier L., Clark N., Dubuque T., Elliston K., Hawkins M., Holman M.,
RA   Hultman M., Kucaba T., Le M., Lennon G., Marra M., Parsons J., Rifkin L.,
RA   Rohlfing T., Soares M., Tan F., Trevaskis E., Waterston R., Williamson A.,
RA   Wohldmann P., Wilson R.;
RT   "The WashU-Merck EST Project";
RL   Unpublished.
XX
DR   RZPD; IMAGp998F03326; IMAGp998F03326.
XX
CC   On May 8, 1995 this sequence version replaced gi:800819.
CC   Contact: Wilson RK
CC   Washington University School of Medicine
CC   4444 Forest Park Parkway, Box 8501, St. Louis, MO 63108
CC   Tel: [phone]
CC   Fax: [phone]
CC   Email: [e-mail]
CC   Insert Size: 544
CC   High quality sequence stops: 265
CC   Source: IMAGE Consortium, LLNL
CC   This clone is available royalty-free through LLNL ; contact the
CC   IMAGE Consortium ([e-mail]) for further information.
CC   Possible reversed clone: polyT not found
CC   Insert Length: 544   Std Error: 0.00
CC   Seq primer: SP6
CC   High quality sequence stop: 265.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..495
FT                   /db_xref="taxon:9606"
FT                   /db_xref="ESTLIB:300"
FT                   /db_xref="RZPD:IMAGp998F03326"
FT                   /note="Organ: brain; Vector: pT7T3D (Pharmacia) with a
FT                   modified polylinker; Site_1: Not I; Site_2: Eco RI; 1st
FT                   strand cDNA was primed with a Not I - oligo(dT) primer [5'
FT                   TGTTACCAATCTGAAGTGGGAGCGGCCGCGCTTTTTTTTTTTTTTTTTTT 3'],
FT                   double-stranded cDNA was size selected, ligated to Eco RI
FT                   adapters (Pharmacia), digested with Not I and cloned into
FT                   the Not I and Eco RI sites of a modified pT7T3 vector
FT                   (Pharmacia). Library went through one round of
FT                   normalization to a Cot = 53. Library constructed by Bento
FT                   Soares and M.Fatima Bonaldo. The adult brain RNA was
FT                   provided by Dr. Donald H. Gilden. Tissue was acquired 17-18
FT                   hours after death which occurred in consequence of a
FT                   ruptured aortic aneurysm. RNA was prepared from a pool of
FT                   tissues representing the following areas of the brain:
FT                   frontal, parietal, temporal and occipital cortex from the
FT                   left and right hemispheres, subcortical white matter, basal
FT                   ganglia, thalamus, cerebellum, midbrain, pons and medulla."
FT                   /sex="Male"
FT                   /organism="Homo sapiens"
FT                   /clone="IMAGE:177794"
FT                   /clone_lib="Soares adult brain N2b5HB55Y"
FT                   /dev_stage="55-year old"
FT                   /lab_host="DH10B (ampicillin resistant)"
XX
SQ   Sequence 495 BP; 73 A; 135 C; 169 G; 104 T; 14 other;
     ccggnaagct cancttggac caccgactct cgantgnntc gccgcgggag ccggntggan        60
     aacctgagcg ggactggnag aaggagcaga gggaggcagc acccggcgtg acggnagtgt       120
     gtggggcact caggccttcc gcagtgtcat ctgccacacg gaaggcacgg ccacgggcag       180
     gggggtctat gatcttctgc atgcccagct ggcatggccc cacgtagagt ggnntggcgt       240
     ctcggtgctg gtcagcgaca cgttgtcctg gctgggcagg tccagctccc ggaggacctg       300
     gggcttcagc ttcccgtagc gctggctgca gtgacggatg ctcttgcgct gccatttctg       360
     ggtgctgtca ctgtccttgc tcactccaaa ccagttcggc ggtccccctg cggatggtct       420
     gtgttgatgg acgtttgggc tttgcagcac cggccgccga gttcatggtn gggtnaagag       480
     atttgggttt tttcn                                                        495
//
</pre>
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<p><h3>Database entry: tembl:hsnfg9</h3>
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<pre>
ID   HSNFG9     standard; DNA; HUM; 33760 BP.
XX
AC   Z69719;
XX
SV   Z69719.1
XX
DT   26-FEB-1996 (Rel. 46, Created)
DT   22-NOV-1999 (Rel. 61, Last updated, Version 3)
XX
DE   Human DNA sequence from cosmid NFG9 from a contig from the tip of the short
DE   arm of chromosome 16, spanning 2Mb of 16p13.3. Contains Interleukin 9
DE   Receptor Pseudogene, repeat polymorphism, ESTs, CpG islands and endogenous
DE   retroviral DNA.
XX
KW   16p13.3; CpG island; Interleukin 9 Receptor Pseudogene;
KW   repeat polymorphism.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-33760
RA   Kershaw J.;
RT   ;
RL   Submitted (22-FEB-1996) to the EMBL/GenBank/DDBJ databases.
RL   Sanger Centre, Hinxton, Cambridgeshire, CB10 1RQ, England. E-mail enquires:
RL   [e-mail]
XX
CC   IMPORTANT:  This sequence is not the entire insert of clone
CC   NFG9.  It may be shorter because we only sequence overlapping
CC   sections once, or longer because we arrange for a small
CC   overlap between neighbouring submissions.
XX
CC   The true left end of clone NFG9 is at 1 in this sequence.
CC   The true left end of clone RA36 is at 25872.
XX
CC   NFG9 is from a 280kb clone contig extending from the telomere of 16p.
CC   Higgs D.R., Flint J. unpublished. MRC Molecular Haematology Unit,
CC   Institute of Molecular Medicine, Oxford.
CC   NFG9 is from the library CV007K. Choo et al.,(1986) Gene 46. 277-286.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..33760
FT                   /chromosome="16"
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /map="16p13.3"
FT                   /clone_lib="CV007K"


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

     gagacagcag agtgctcagc tcatgaagga ggcaccagcc gccatgcctc tacatccagg     30840
     tctcctgggg ttcccacctc cacaaaaacc cccactgcta ggagtgcagg caggagggga     30900
     cctgagaacc gacagttata ggtcctgcgg gtgggcagtg ctgggtgttc tggtctgccc     30960
     cacccctgtg tgcctagatc cccatctggg cctcaagtgg gtgggattcc aaaggaagag     31020
     ccggagtagg cgtggggagg ggcaggccca ggctggacaa agagtctggc cagggagcgg     31080
     cacattgccc tcccagagac agtggctcag tgtccaggcc ttccccaggc gcacagtggg     31140
     ctcttgttcc cagaaagccc ctcgggggga tccaaacagt gtctccccca ccccgctgac     31200
     ccctcagtgt atggggaaac cgtggcccac ggaaggcctc actgcctggg gtcacacagc     31260
     atctgagtca ctgcagcagc ctcacagctg ccagcccagg cccagcccca tcaggagaca     31320
     cccaaagcca cagtgcatcc caggaccagc tgggggggct gcgggcagga ctctcgatga     31380
     ggctgaggga cgaggagggt caagggagcc actggcgcca tgcatgctga cgtcccctct     31440
     ggctgcctgc agagcctggt gtggaagggc tgagtggggg atggtggaga gtcctgttaa     31500
     ctcaggtttc tgctctgggg atgtctgggc acccatcaag ctggccgcgt gcacaggtgc     31560
     agggagagcc agaaagcagg agccgatgca gggaggccac tggggacagc ccaggctgat     31620
     gcttgggccc catgtgtctc caccacctac aaccctaagc aagcctcagc tttcccatct     31680
     ggaaatcagg ggtcacagca gtgcctggca cagtagcagc ggctgactcc atcacagggt     31740
     ggtgtagcct gtgggtactt ggcactctct gaggggcagg agctgggggg tgaaaggacc     31800
     ctagagcata tgcaacaaga gggcagccct ggggacacct ggggacagaa ccctccaaag     31860
     gtgtcgagtt tgggaagaga ctagagagaa gctctggcca gtccaggcat agacagtggc     31920
     cacagccagt ggagagctgc atcctcaggt gtgagcagca accacctctg tactcaggcc     31980
     tgccctgcac actcacagga ccatgctggc agggacaact ggcggcggag ttgactgcca     32040
     accccggggc cagaaccatc aagcctgggc tctgctccgc ccaaggaact gcctgctgcc     32100
     gaggtcagct ggagcaaggg gcctcacccc gggacacctt cccagacgtg tcctcagctc     32160
     acatgagcct catcccaggg ggatgtggct cctccagcat ccccacccac acgctgctct     32220
     ctgaccctca gtcttctgtt tgactcctaa tctgaagctc aatcctagat ctcccttgag     32280
     aagggggtca ccagctgtct ggcagcccag cctccaggtc ttctggatta atgaagggaa     32340
     agtcacctgg cctctctgcc ttgtctatta atggcatcat gctgagaatg atatttgcta     32400
     ggccctttgc aaaccccaaa gtgctcttca accctcccag tgaagcctct tcttttctgt     32460
     ggaagaaatg aggttcaggg tggagcaggg caggcctgag acctttgcag ggttctctcc     32520
     aggtccccag caggacagac tggcaccctg cctcccctca tcaccctaga caaggagaca     32580
     gaacaagagg ttccctgcta caggccatct gtgagggaag ccgccctagg gcctgtagac     32640
     acaggaatcc ctgaggacct gacctgtgag ggtagtgcac aaaggggcca gcacttggca     32700
     ggaggggggg gggcactgcc ccaaggctca gctagcaaat gtggcacagg ggtcaccaga     32760
     gctaaacccc tgactcagtt gggtctgaca ggggctgaca tggcagacac acccaggaat     32820
     caggggacac caagtgcagc tcagggcacc tgtccaggcc acacagtcag aaaggggatg     32880
     gcagcaagga cttagctaca ctagattctg ggggtaaact gcctggtatg ctggtcactg     32940
     ctagtcccca gtctggagtc tagctgggtc tcaggagtta ggcgaaaaca ccctccccag     33000
     gctgcaggtg ggagaggccc acatcccctg cacacgtctg gccagaggac agatgggcag     33060
     cccagtcacc agtcagagcc ctccagaggt gtccctgact gaccctacac acatgcaccc     33120
     aggtgcccag gcacccttgg gctcagcaac cctgcaaccc cctcccagga cccaccagaa     33180
     gcaggatagg actagagagg ccacaggagg gaaaccaagt cagagcagaa atggcttcgg     33240
     tcctcagcag cctggctcag cttcctcaaa ccagatcctg actgatcaca ctggtctgtc     33300
     taacccctgg gaggggtcct ctgtatccat cttacagata aggaaactga ggctcagaga     33360
     agcccatcac tgcctaaggt cccagggcct ataagggagc tcaaagcctt gggccaggtc     33420
     tgcccaggag ctgcagtgga agggaccctg tctgcagacc cccagaagac aaggcagacc     33480
     acctgggttc ttcagccttg tggctgtgga cggctgtcag acccttctaa gaccccttgc     33540
     cacctgctcc atcaggggca tctcagttga agaaggaagg actcaccccc aaaatcgtcc     33600
     aactcagaaa aaaaggcaga agccaaggaa tccaatcact gggcaaaatg tgatcctggc     33660
     acagacactg aggtggggga actggagccg gtgtggcgga ggccctcaca gccaagagca     33720
     actgggggtg ccctgggcag ggactgtagc tgggaagatc                           33760
//
</pre>
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