[SE-260] cleanup

SVN: 17553

plasmid/PRS316.gb

-ID   PRS316     preliminary; circular DNA; SYN; 4887 BP.
-XX
-AC   U03442; ATCC77145;
-XX
-DT   01-JUL-1993 (Rel. 7, Created)
-DT   01-JUL-1995 (Rel. 12, Last updated, Version 1)
-XX
-DE   Saccharomyces/E.coli phagemid vector pRS316 - complete.
-XX
-KW   cloning vector.
-XX
-OS   Cloning vector
-OC   Artificial sequences; Cloning vehicles.
-XX
-RN   [1]
-RP   1-4887
-RC   pRSS56 from pBluescript KS+ & BlueScribe
-RC   pRS303 from pRSS56 & HIS3 gene
-RC   pRS304 from pRSS56 & TRP1 gene
-RC   pRS305 from pRSS56 & LEU2 gene
-RC   pRS306 from pRSS56 & URA3 gene
-RC   pUC19-CEN6:32 from pUC19 & CEN6
-RC   pRSS83 from pUC19-CEN6:32 & pAB9, ARS
-RC   pRSS84 from pRSS83
-RC   pRS313 from pRS303 & pRSS84
-RC   pRS314 from pRS304 & pRSS84
-RC   pRS315 from pRS305 & pRSS84
-RC   pRS316 from pRS306 & pRSS84
-RC   pRSS93 from pRSS84 & pYCF5
-RA   Sikorski R.S., Hieter P.;
-RT   "A system of shuttle vectors and yeast host strains designed for
-RT   efficient manipulation of DNA in Saccharomyces cerevisiae";
-RL   Genetics 122:19-27(1989).
-XX
-RN   [2]
-RC   from YEp24
-RC   from YCp50
-RC   from YIp5
-RA   Strathern J.N., Higgins D.R.;
-RT   "Recovery of plasmids from yeast into Escherichia coli: shuttle
-RT   vectors";
-RL   Meth. Enzymol. 194:319-329(1991).
-XX
-RN   [3]
-RC   pRS316
-RA   Stillman D.J.;
-RT   ;
-RL   Submitted (10-NOV-1993) by:
-RL   Stillman D.J., Dept. of Cellular, Viral and Molecular Biology,
-RL   University of Utah Medical Center, Salt Lake City, UT 84132 USA.
-XX
-CC   One of a series of pBluescript-based centromere vectors (ATCC 77142
-CC   ATCC 77145, ATCC 77157 to ATCC 77158) differing in the yeast
-CC   selectable marker gene. [1]
-CC   The order of the major features in this plasmid is: URA3 - f1 ori
-CC   (NaeI) - T7 promoter - lacZ'/MCS - T3 promoter - pMB1 ori - bla -
-CC   CEN6 - ARSH4.
-CC   A fragment (1.112 kb) containing the URA3 gene was inserted into the
-CC   NdeI site and a cassette containing CEN6 and the ARS associated with
-CC   histone 4 (ARSH4) was inserted into the AatII site of pRSS56. All ends
-CC   were blunted.
-CC   pRSS56, constructed by ligating a PvuI fragment (bp 498-2412) of
-CC   pBluescript KS+ to a PvuI fragment (bp 2850-730) of pBS(+), contains
-CC   the KS MCS from pBluescript KS+ and the unique NdeI and AatII sites
-CC   between bla and f1 origin of pBS(+). [1]
-CC   YC-type centromere vector permitting visual detection of recombinants
-CC   and production of ssDNA in E.coli.  Contains promoters for in vitro
-CC   RNA synthesis, priming sites useful for sequencing, and encodes the
-CC   lacZ alpha (lacZ') peptide. [1]
-CC   Useful in plasmid shuffle experiments.
-CC   Restriction digests of the clone give the following sizes (kb):
-CC   EcoRI--5.0; BamHI--5.0, PvuII--4.4, 0.5. (ATCC staff)
-CC   Medium is 1227 LB plus ampicillin.
-CC   NCBI gi: 417973
-CC   NM (pRS316)
-CC   CM (yes)
-CC   NA (ds-DNA)
-CC   TP (circular)
-CC   ST ()
-CC   TY (phagemid)
-CC   SP (ATCC)
-CC   HO (E.coli HB101)(Saccharomyces cerevisiae)(E.coli)
-CC   HO (Saccharomyces cerevisiae YPH499)(Saccharomyces cerevisiae YPH500)
-CC   HO (Saccharomyces cerevisiae YPH501)
-CC   CP ()
-CC   FN (cloning)
-CC   SE ()
-CC   PA ()
-CC   BR (pRS314)(pRS315)(pRS313)
-CC   OF ()
-CC   OR ()
-XX
-FH   Key             Location/Qualifiers
-FH
-FT   misc_feature    0..0
-FT                   /note="1. pUC19 HincII 2686bp 432..432
-FT                   2. yeast MboII-MboII 125bp, CEN6
-FT                   -> pUC19-CEN6:32 2811bp
-FT                   1. pUC8 BamHI 2665bp 241..241
-FT                   2. yeast Sau3AI-Sau3AI 374bp, histone H4 ARS/ARSH4
-FT                   -> pAB9 3039bp
-FT                   1. pUC19-CEN6:32 EcoRI-ScaI 1908bp 397..-..2180, CEN6
-FT                   2. pAB9 ScaI-EcoRI 1314bp 231..-..1171,
-FT                   \ histone H4 ARS/ARSH4
-FT                   -> pRSS83 3222bp [in MCS]
-FT                   1. pRSS83 remove SmaI-XbaI 9bp, MCS/pUC19 415..424
-FT                   \ 3213bp
-FT                   Klenow:Klenow
-FT                   -> pRSS84 3213bp
-FT                   1. pRSS84 HincII-PstI, CEN6/ARSH4
-FT                   \ pUC19 440..2686..432
-FT                   T4 DNA polymerase:T4 DNA polymerase
-FT                   2. pRS306 AatII 4373bp 848..848
-FT                   T4 DNA polymerase:T4 DNA polymerase
-FT                   -> pRS316 4887bp"
-FT   misc_binding    0..0
-FT                   /note="MCS KpnI-ApaI-XhoI-SalI-ClaI-HindIII-EcoRV-
-FT                   EcoRI-PstI-SmaI-
-FT                   BamHI-SpeI-XbaI-EagI-NotI-BstXI-SacII-SacI"
-FT   misc_binding    0..0
-FT                   /note="SIT unique KpnI-ApaI-XhoI-SalI-ClaI-EcoRI-
-FT                   PstI-SmaI-BamHI-SpeI-EagI-NotI-SacII-SacI-NaeI"
-FT   rep_origin      0..0
-FT                   /note="ORI E. coli pMB1 (ColE1 and pBR322)"
-FT   rep_origin      0..0
-FT                   /note="ORI bacteriophage f1"
-FT   promoter        0..0
-FT                   /note="PRO E. coli lac gene"
-FT   promoter        0..0
-FT                   /note="PRO bacteriophage T3"
-FT   promoter        0..0
-FT                   /note="PRO bacteriophage T7"
-FT   CDS             0..0
-FT                   /note="GEN E. coli beta-galactosidase gene (lacZ');
-FT                   reporter gene"
-FT   CDS             0..0
-FT                   /note="ANT E. coli beta-lactamase gene (bla)
-FT                   ampicillin resistance gene (apr/amp)"
-FT   CDS             0..0
-FT                   /note="ANT yeast URA3 gene"
-FT   rep_origin      0..0
-FT                   /note="ORI yeast ARSH4"
-FT   misc_feature    0..0
-FT                   /note="yeast centromere CEN6"
-XX
-SQ   Sequence 4887 BP; 1361 A; 1069 C; 1167 G; 1290 T; 0 other;
-     tcgcgcgttt cggtgatgac ggtgaaaacc tctgacacat gcagctcccg gagacggtca
-     cagcttgtct gtaagcggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtg
-     ttggcgggtg tcggggctgg cttaactatg cggcatcaga gcagattgta ctgagagtgc
-     accacgcttt tcaattcaat tcatcatttt ttttttattc ttttttttga tttcggtttc
-     tttgaaattt ttttgattcg gtaatctccg aacagaagga agaacgaagg aaggagcaca
-     gacttagatt ggtatatata cgcatatgta gtgttgaaga aacatgaaat tgcccagtat
-     tcttaaccca actgcacaga acaaaaacct gcaggaaacg aagataaatc atgtcgaaag
-     ctacatataa ggaacgtgct gctactcatc ctagtcctgt tgctgccaag ctatttaata
-     tcatgcacga aaagcaaaca aacttgtgtg cttcattgga tgttcgtacc accaaggaat
-     tactggagtt agttgaagca ttaggtccca aaatttgttt actaaaaaca catgtggata
-     tcttgactga tttttccatg gagggcacag ttaagccgct aaaggcatta tccgccaagt
-     acaatttttt actcttcgaa gacagaaaat ttgctgacat tggtaataca gtcaaattgc
-     agtactctgc gggtgtatac agaatagcag aatgggcaga cattacgaat gcacacggtg
-     tggtgggccc aggtattgtt agcggtttga agcaggcggc agaagaagta acaaaggaac
-     ctagaggcct tttgatgtta gcagaattgt catgcaaggg ctccctatct actggagaat
-     atactaaggg tactgttgac attgcgaaga gcgacaaaga ttttgttatc ggctttattg
-     ctcaaagaga catgggtgga agagatgaag gttacgattg gttgattatg acacccggtg
-     tgggtttaga tgacaaggga gacgcattgg gtcaacagta tagaaccgtg gatgatgtgg
-     tctctacagg atctgacatt attattgttg gaagaggact atttgcaaag ggaagggatg
-     ctaaggtaga gggtgaacgt tacagaaaag caggctggga agcatatttg agaagatgcg
-     gccagcaaaa ctaaaaaact gtattataag taaatgcatg tatactaaac tcacaaatta
-     gagcttcaat ttaattatat cagttattac cctgcggtgt gaaataccgc acagatgcgt
-     aaggagaaaa taccgcatca ggaaattgta aacgttaata ttttgttaaa attcgcgtta
-     aatttttgtt aaatcagctc attttttaac caataggccg aaatcggcaa aatcccttat
-     aaatcaaaag aatagaccga gatagggttg agtgttgttc cagtttggaa caagagtcca
-     ctattaaaga acgtggactc caacgtcaaa gggcgaaaaa ccgtctatca gggcgatggc
-     ccactacgtg aaccatcacc ctaatcaagt tttttggggt cgaggtgccg taaagcacta
-     aatcggaacc ctaaagggag cccccgattt agagcttgac ggggaaagcc ggcgaacgtg
-     gcgagaaagg aagggaagaa agcgaaagga gcgggcgcta gggcgctggc aagtgtagcg
-     gtcacgctgc gcgtaaccac cacacccgcc gcgcttaatg cgccgctaca gggcgcgtcg
-     cgccattcgc cattcaggct gcgcaactgt tgggaagggc gatcggtgcg ggcctcttcg
-     ctattacgcc agctggcgaa ggggggatgt gctgcaaggc gattaagttg ggtaacgcca
-     gggttttccc agtcacgacg ttgtaaaacg acggccagtg aattgtaata cgactcacta
-     tagggcgaat tggagctcca ccgcggtggc ggccgctcta gaactagtgg atcccccggg
-     ctgcaggaat tcgatatcaa gcttatcgat accgtcgacc tcgagggggg gcccggtacc
-     cagcttttgt tccctttagt gagggttaat tccgagcttg gcgtaatcat ggtcatagct
-     gtttcctgtg tgaaattgtt atccgctcac aattccacac aacataggag ccggaagcat
-     aaagtgtaaa gcctggggtg cctaatgagt gaggtaactc acattaattg cgttgcgctc
-     actgcccgct ttccagtcgg gaaacctgtc gtgccagctg cattaatgaa tcggccaacg
-     cgcggggaga ggcggtttgc gtattgggcg ctcttccgct tcctcgctca ctgactcgct
-     gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
-     atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
-     caggaaccgt aaaaaggccg cgttgctggc gtttttccat aggctcggcc cccctgacga
-     gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
-     ccaggcgttc ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
-     cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcaat gctcacgctg
-     taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
-     cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
-     acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
-     aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaaggacagt
-     atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
-     atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
-     gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
-     gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
-     ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
-     ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
-     tcgttcatcc atagttgcct gactgcccgt cgtgtagata actacgatac gggagggctt
-     accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
-     atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
-     cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
-     tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
-     tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
-     gtgaaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
-     agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
-     aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
-     gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
-     tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
-     gctgttgaga tccagttcga tgtaacccac tcgtgcaccc aactgatctt cagcatcttt
-     tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
-     aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
-     catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
-     acaaataggg gttccgcgca catttccccg aaaagtgcca cctgggtcct tttcatcacg
-     tgctataaaa ataattataa tttaaatttt ttaatataaa tatataaatt aaaaatagaa
-     agtaaaaaaa gaaattaaag aaaaaatagt ttttgttttc cgaagatgta aaagactcta
-     gggggatcgc caacaaatac taccttttat cttgctcttc ctgctctcag gtattaatgc
-     cgaattgttt catcttgtct gtgtagaaga ccacacacga aaatcctgtg attttacatt
-     ttacttatcg ttaatcgaat gtatatctat ttaatctgct tttcttgtct aataaatata
-     tatgtaaagt acgctttttg ttgaaatttt ttaaaccttt gtttattttt ttttcttcat
-     tccgtaactc ttctaccttc tttatttact ttctaaaatc caaatacaaa acataaaaat
-     aaataaacac agagtaaatt cccaaattat tccatcatta aaagatacga ggcgcgtgta
-     agttacaggc aagcgatccg tcctaagaaa ccattattat catgacatta acctataaaa
-     ataggcgtat cacgaggccc tttcgtc
-//

plasmid/resource/recreate_db.sh

-OWNER=buczekp
-psql -U postgres -c "drop database openbis_plasmids;"
-psql -U postgres -c "create database openbis_plasmids with owner $OWNER encoding = 'UNICODE';"
-psql -U $OWNER -d openbis_plasmids -f plasmids-YeastLab.sql 

plasmid/source/java/ch/ethz/bsse/cisd/plasmid/plasmapper/PlasMapperUploader.java

@@ -133,7 +133,7 @@ public class PlasMapperUploader
     {
         final Properties p = createDefaultProperties();
         final PlasMapperUploader uploader = new PlasMapperUploader(DEFAULT_PLASMAPPER_URL, p);
-        final File seqFile = new File("PRS316.gb");
+        final File seqFile = new File("resource/example/FRP_1/PRS316.gb");
         for (PlasMapperService service : PlasMapperService.values())
         {
             String response = uploader.upload(seqFile, service);